April 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Update argument names to parameter help for GATK Advanced options.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/99b2fe57e167/ changeset: 99b2fe57e167 user: dan date: 2012-04-10 17:46:46 summary: Update argument names to parameter help for GATK Advanced options. affected #: 15 files diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -215,17 +215,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -327,20 +327,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -355,10 +355,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -369,34 +369,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,17 +239,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -351,20 +351,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -379,10 +379,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -393,34 +393,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -179,17 +179,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -291,20 +291,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -319,10 +319,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -333,34 +333,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,17 +147,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -259,20 +259,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -287,10 +287,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -301,34 +301,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -165,17 +165,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -277,20 +277,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -305,10 +305,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -319,34 +319,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,17 +154,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -266,20 +266,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -294,10 +294,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -308,34 +308,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -220,17 +220,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -332,20 +332,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -360,10 +360,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -374,34 +374,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,17 +245,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -357,20 +357,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -385,10 +385,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -399,34 +399,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,17 +135,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -247,20 +247,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -275,10 +275,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -289,34 +289,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,17 +155,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -267,20 +267,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -295,10 +295,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -309,34 +309,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,17 +211,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -323,20 +323,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -351,10 +351,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -365,34 +365,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,17 +164,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -276,20 +276,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -304,10 +304,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -318,34 +318,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -370,17 +370,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -482,20 +482,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -510,10 +510,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -524,34 +524,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,17 +209,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -321,20 +321,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -349,10 +349,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -363,34 +363,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,17 +135,17 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option> @@ -247,20 +247,20 @@ </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option> @@ -275,10 +275,10 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when> @@ -289,34 +289,34 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Apr '12

10 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e780ec798c93/ changeset: e780ec798c93 user: jgoecks date: 2012-04-10 17:19:47 summary: Backbone UI enhancements: create collection of tools in tool panel and use to get model when a tool link is clicked. affected #: 1 file diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r e780ec798c9373e475d2bc698c0d991fc7baa166 static/scripts/backbone/tools.js --- a/static/scripts/backbone/tools.js +++ b/static/scripts/backbone/tools.js @@ -45,6 +45,13 @@ }); /** + * Wrap collection of tools for fast access/manipulation. + */ +var ToolCollection = Backbone.Collection.extend({ + model: Tool +}); + +/** * Label or section header in tool panel. */ var ToolPanelLabel = BaseModel.extend({}); @@ -149,6 +156,8 @@ */ var ToolPanel = Backbone.Collection.extend({ url: "/tools", + tools: new ToolCollection(), + parse: function(response) { // Recursive function to parse tool panel elements. var parse_elt = function(elt_dict) { @@ -173,6 +182,27 @@ initialize: function(options) { this.tool_search = options.tool_search; this.tool_search.on("change:results", this.apply_search_results, this); + this.on("reset", this.populate_tools, this); + }, + + /** + * Populate tool collection from panel elements. + */ + populate_tools: function() { + var self = this; + self.tools = new ToolCollection(); + this.each(function(panel_elt) { + if (panel_elt instanceof ToolPanelSection) { + _.each(panel_elt.attributes.elems, function (section_elt) { + if (section_elt instanceof Tool) { + self.tools.push(section_elt); + } + }); + } + else if (panel_elt instanceof Tool) { + self.tools.push(panel_elt); + } + }); }, clear_search_results: function() { @@ -358,34 +388,51 @@ */ initialize: function(options) { this.collection.tool_search.on("change:results", this.handle_search_results, this); + + this.tool_link_click_fn = null; + if (options && 'tool_link_click_fn' in options) { + this.tool_link_click_fn = options.tool_link_click_fn; + } }, render: function() { - var this_el = this.$el; + var self = this; // Render search. var search_view = new ToolSearchView( {model: this.collection.tool_search} ); search_view.render(); - this_el.append(search_view.$el); + self.$el.append(search_view.$el); // Render panel. this.collection.each(function(panel_elt) { if (panel_elt instanceof ToolPanelSection) { var section_title_view = new ToolPanelSectionView({model: panel_elt}); section_title_view.render(); - this_el.append(section_title_view.$el); + self.$el.append(section_title_view.$el); } else if (panel_elt instanceof Tool) { var tool_view = new ToolLinkView({model: panel_elt, className: "toolTitleNoSection"}); tool_view.render(); - this_el.append(tool_view.$el); + self.$el.append(tool_view.$el); } else if (panel_elt instanceof ToolPanelLabel) { var label_view = new ToolPanelLabelView({model: panel_elt}); label_view.render(); - this_el.append(label_view.$el); + self.$el.append(label_view.$el); } }); + + // Setup tool link click handling. + if (self.tool_link_click_fn) { + self.$el.find("a.tool-link").click(function() { + // Tool id is always the first class. + var tool_id = $(this).attr('class').split(/\s+/)[0]; + + self.tool_link_click_fn(self.collection.tools.get(tool_id)); + return false; + }); + } + return this; }, https://bitbucket.org/galaxy/galaxy-central/changeset/bc94cf3ea6d0/ changeset: bc94cf3ea6d0 user: jgoecks date: 2012-04-10 17:21:37 summary: Merge affected #: 15 files diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -180,13 +180,13 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="mask">Mask</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /></when> @@ -215,204 +215,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,204 +239,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -996,25 +996,25 @@ **Settings**:: - calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. - ignoreDeletionSites boolean false Ignore sites consisting only of deletions - includeDeletions boolean false Include information on deletions - maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). - maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). - minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. - minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. - nBins int 499 Number of bins to use for granular binning - omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup - omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup - omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup - omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. - outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table - partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. - printBaseCounts boolean false Will add base counts to per-locus output. - printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. - start int 1 Starting (left endpoint) for granular binning - stop int 500 Ending (right endpoint) for granular binning - summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. + calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. + ignoreDeletionSites boolean false Ignore sites consisting only of deletions + includeDeletions boolean false Include information on deletions + maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). + maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). + minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. + minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. + nBins int 499 Number of bins to use for granular binning + omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup + omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup + omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup + omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. + outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table + partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. + printBaseCounts boolean false Will add base counts to per-locus output. + printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. + start int 1 Starting (left endpoint) for granular binning + stop int 500 Ending (right endpoint) for granular binning + summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. ------ diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -146,12 +146,12 @@ <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /><repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -179,204 +179,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,204 +147,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -407,11 +407,11 @@ **Settings**:: - number int -1 Print the first n reads from the file, discarding the rest - platform String NA Exclude all reads with this platform from the output - readGroup String NA Exclude all reads with this read group from the output - sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times - sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. + number int -1 Print the first n reads from the file, discarding the rest + platform String NA Exclude all reads with this platform from the output + readGroup String NA Exclude all reads with this read group from the output + sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times + sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. ------ diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -134,12 +134,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -165,204 +165,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,204 +154,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -179,12 +179,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -220,204 +220,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -464,13 +464,13 @@ <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" /><param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /> - <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options> - </param> + </param><repeat name="additional_annotations" title="Additional annotation"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> @@ -488,14 +488,14 @@ </when></conditional> --> - <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option> -  - </param> +  + </param><param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,204 +245,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,204 +155,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,204 +211,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,204 +164,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -177,7 +177,7 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> + <option value="dbsnp" selected="True">dbSNP</option><option value="variant">Variants</option><option value="snps">SNPs</option><option value="indels">INDELs</option> @@ -370,204 +370,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,204 +209,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r e780ec798c9373e475d2bc698c0d991fc7baa166 -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add argument names to parameter help for GATK Advanced options.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5921f5fed6de/ changeset: 5921f5fed6de user: dan date: 2012-04-10 17:20:12 summary: Add argument names to parameter help for GATK Advanced options. affected #: 15 files diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -180,13 +180,13 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="mask">Mask</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="mask">Mask</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /></when> @@ -215,204 +215,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -239,204 +239,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -996,25 +996,25 @@ **Settings**:: - calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. - ignoreDeletionSites boolean false Ignore sites consisting only of deletions - includeDeletions boolean false Include information on deletions - maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). - maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). - minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. - minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. - nBins int 499 Number of bins to use for granular binning - omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup - omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup - omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup - omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. - outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table - partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. - printBaseCounts boolean false Will add base counts to per-locus output. - printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. - start int 1 Starting (left endpoint) for granular binning - stop int 500 Ending (right endpoint) for granular binning - summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. + calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. + ignoreDeletionSites boolean false Ignore sites consisting only of deletions + includeDeletions boolean false Include information on deletions + maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). + maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). + minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. + minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. + nBins int 499 Number of bins to use for granular binning + omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup + omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup + omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup + omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. + outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table + partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. + printBaseCounts boolean false Will add base counts to per-locus output. + printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. + start int 1 Starting (left endpoint) for granular binning + stop int 500 Ending (right endpoint) for granular binning + summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. ------ diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -146,12 +146,12 @@ <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" /><repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -179,204 +179,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -147,204 +147,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -407,11 +407,11 @@ **Settings**:: - number int -1 Print the first n reads from the file, discarding the rest - platform String NA Exclude all reads with this platform from the output - readGroup String NA Exclude all reads with this read group from the output - sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times - sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. + number int -1 Print the first n reads from the file, discarding the rest + platform String NA Exclude all reads with this platform from the output + readGroup String NA Exclude all reads with this read group from the output + sample_file Set[File] [] File containing a list of samples (one per line). Can be specified multiple times + sample_name Set[String] [] Sample name to be included in the analysis. Can be specified multiple times. ------ diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -134,12 +134,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -165,204 +165,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -154,204 +154,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -179,12 +179,12 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> - <option value="snps">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> + <param name="rod_bind_type_selector" type="select" label="Binding Type"> + <option value="dbsnp" selected="True">dbSNP</option> + <option value="snps">SNPs</option> + <option value="indels">INDELs</option> + <option value="custom">Custom</option> + </param><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /></when> @@ -220,204 +220,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> @@ -464,13 +464,13 @@ <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" /><param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /> - <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"><options from_data_table="gatk_annotations"><filter type="multiple_splitter" column="tools_valid_for" separator=","/><filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/></options> - </param> + </param><repeat name="additional_annotations" title="Additional annotation"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> @@ -488,14 +488,14 @@ </when></conditional> --> - <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> + <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option> -  - </param> +  + </param><param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -245,204 +245,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -155,204 +155,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -211,204 +211,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -164,204 +164,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -177,7 +177,7 @@ <repeat name="rod_bind" title="Binding for reference-ordered data"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="dbsnp" selected="True">dbSNP</option> + <option value="dbsnp" selected="True">dbSNP</option><option value="variant">Variants</option><option value="snps">SNPs</option><option value="indels">INDELs</option> @@ -370,204 +370,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -209,204 +209,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> diff -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad -r 5921f5fed6de61a11c68d403e56c80bc17db3f86 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -135,204 +135,204 @@ </when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples" /> + <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat> - <repeat name="pedigree_string_repeat" title="Pedigree string"> - <param name="pedigree_string" type="text" value="" label="Pedigree string for samples" /> + <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>"> + <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat> - <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information"> + <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param> - <repeat name="read_filter" title="Read Filter"> + <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="BadCigar">BadCigar</option> - <option value="BadMate">BadMate</option> - <option value="DuplicateRead">DuplicateRead</option> - <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> - <option value="MalformedRead">MalformedRead</option> - <option value="MappingQuality">MappingQuality</option> - <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> - <option value="MappingQualityZero">MappingQualityZero</option> - <option value="MateSameStrand">MateSameStrand</option> - <option value="MaxInsertSize">MaxInsertSize</option> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="MissingReadGroup">MissingReadGroup</option> - <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> - <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> - <option value="Platform454">Platform454</option> - <option value="Platform">Platform</option> - <option value="PlatformUnit">PlatformUnit</option> - <option value="ReadGroupBlackList">ReadGroupBlackList</option> - <option value="ReadName">ReadName</option> - <option value="ReadStrand">ReadStrand</option> - <option value="ReassignMappingQuality">ReassignMappingQuality</option> - <option value="Sample">Sample</option> - <option value="SingleReadGroup">SingleReadGroup</option> - <option value="UnmappedRead">UnmappedRead</option> - </param> - <when value="BadCigar"> -  - </when> - <when value="BadMate"> -  - </when> - <when value="DuplicateRead"> -  - </when> - <when value="FailsVendorQualityCheck"> -  - </when> - <when value="MalformedRead"> -  - </when> - <when value="MappingQuality"> - <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> - </when> - <when value="MappingQualityUnavailable"> -  - </when> - <when value="MappingQualityZero"> -  - </when> - <when value="MateSameStrand"> -  - </when> - <when value="MaxInsertSize"> - <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> - <when value="MissingReadGroup"> -  - </when> - <when value="NoOriginalQualityScores"> -  - </when> - <when value="NotPrimaryAlignment"> -  - </when> - <when value="Platform454"> -  - </when> - <when value="Platform"> - <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> - </when> - <when value="PlatformUnit"> -  - </when> - <when value="ReadGroupBlackList"> -  - </when> - <when value="ReadName"> - <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> - </when> - <when value="ReadStrand"> - <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> - </when> - <when value="ReassignMappingQuality"> - <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> - </when> - <when value="Sample"> - <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> - </when> - <when value="SingleReadGroup"> - <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> - </when> - <when value="UnmappedRead"> -  - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="BadCigar">BadCigar</option> + <option value="BadMate">BadMate</option> + <option value="DuplicateRead">DuplicateRead</option> + <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option> + <option value="MalformedRead">MalformedRead</option> + <option value="MappingQuality">MappingQuality</option> + <option value="MappingQualityUnavailable">MappingQualityUnavailable</option> + <option value="MappingQualityZero">MappingQualityZero</option> + <option value="MateSameStrand">MateSameStrand</option> + <option value="MaxInsertSize">MaxInsertSize</option> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="MissingReadGroup">MissingReadGroup</option> + <option value="NoOriginalQualityScores">NoOriginalQualityScores</option> + <option value="NotPrimaryAlignment">NotPrimaryAlignment</option> + <option value="Platform454">Platform454</option> + <option value="Platform">Platform</option> + <option value="PlatformUnit">PlatformUnit</option> + <option value="ReadGroupBlackList">ReadGroupBlackList</option> + <option value="ReadName">ReadName</option> + <option value="ReadStrand">ReadStrand</option> + <option value="ReassignMappingQuality">ReassignMappingQuality</option> + <option value="Sample">Sample</option> + <option value="SingleReadGroup">SingleReadGroup</option> + <option value="UnmappedRead">UnmappedRead</option> + </param> + <when value="BadCigar"> +  + </when> + <when value="BadMate"> +  + </when> + <when value="DuplicateRead"> +  + </when> + <when value="FailsVendorQualityCheck"> +  + </when> + <when value="MalformedRead"> +  + </when> + <when value="MappingQuality"> + <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> + </when> + <when value="MappingQualityUnavailable"> +  + </when> + <when value="MappingQualityZero"> +  + </when> + <when value="MateSameStrand"> +  + </when> + <when value="MaxInsertSize"> + <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when> + <when value="MissingReadGroup"> +  + </when> + <when value="NoOriginalQualityScores"> +  + </when> + <when value="NotPrimaryAlignment"> +  + </when> + <when value="Platform454"> +  + </when> + <when value="Platform"> + <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/> + </when> + <when value="PlatformUnit"> +  + </when> + <when value="ReadGroupBlackList"> +  + </when> + <when value="ReadName"> + <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/> + </when> + <when value="ReadStrand"> + <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/> + </when> + <when value="ReassignMappingQuality"> + <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/> + </when> + <when value="Sample"> + <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/> + </when> + <when value="SingleReadGroup"> + <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/> + </when> + <when value="UnmappedRead"> +  + </when></conditional></repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat> - <param name="interval_set_rule" type="select" label="Interval set rule"> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type"> - <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> -  - </when> +  + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Downsample method"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/> + </when> + </conditional> + </when></conditional> - <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"> + <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> - <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /> - <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/> - <param name="validation_strictness" type="select" label="How strict should we be with validation"> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" /> + <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" /> + <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/> + <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option></param> - <param name="interval_merging" type="select" label="Interval merging rule"> + <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging <interval_merging>"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <repeat name="read_group_black_list_repeat" title="Read group black list"> + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option><option value="text">Specify filters as a string</option></param><when value="file"> - <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> - </when> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when><when value="text"> - <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> - </when> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when></conditional></repeat> - <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False"/> - <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" /> + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> + <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/></when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: richard_burhans: add column names
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/639548ab15fd/ changeset: 639548ab15fd user: richard_burhans date: 2012-04-10 17:03:11 summary: add column names affected #: 1 file diff -r 04d40a6eca75a9585a874736d799b5bc9869b289 -r 639548ab15fdd83771abb5f1cf7282f7d1cddcad lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -23,6 +23,7 @@ MetadataElement( name="comment_lines", default=0, desc="Number of comment lines", readonly=False, optional=True, no_value=0 ) MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 ) MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) + MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, no_value=[] ) def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) @@ -179,6 +180,9 @@ def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ): out = [] try: + if not column_names and dataset.metadata.column_names: + column_names = dataset.metadata.column_names + column_headers = [None] * dataset.metadata.columns # fill in empty headers with data from column_names Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Small fixes for Trackster icons
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04d40a6eca75/ changeset: 04d40a6eca75 user: jgoecks date: 2012-04-10 15:28:07 summary: Small fixes for Trackster icons affected #: 2 files diff -r e5182b8038e8618529594dea85bc3f304e51a11c -r 04d40a6eca75a9585a874736d799b5bc9869b289 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -80,6 +80,10 @@ .filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} .remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} .icon-button.remove-icon:hover,.overview-close:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} +.icon-button.toggle{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;margin-right:0px;} +.icon-button.toggle:hover{background:transparent url(../images/fugue/toggle.png) no-repeat;} +.icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;margin-right:0px;} +.icon-button.toggle-expand:hover{background:transparent url(../images/fugue/toggle-expand.png) no-repeat;} .icon-button.cross-circle{background:transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px;} .icon-button.cross-circle:hover{background:transparent url(../images/fugue/cross-circle.png) no-repeat;} .icon-button.plus-button{background:transparent url(../images/fugue/plus-button-bw.png) no-repeat;} diff -r e5182b8038e8618529594dea85bc3f304e51a11c -r 04d40a6eca75a9585a874736d799b5bc9869b289 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -393,6 +393,18 @@ .icon-button.remove-icon:hover, .overview-close:hover { background: transparent url(../images/fugue/cross-circle.png) no-repeat; } +.icon-button.toggle { + background: transparent url(../images/fugue/toggle-bw.png) no-repeat;margin-right:0px; +} +.icon-button.toggle:hover { + background: transparent url(../images/fugue/toggle.png) no-repeat; +} +.icon-button.toggle-expand { + background: transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;margin-right:0px; +} +.icon-button.toggle-expand:hover { + background: transparent url(../images/fugue/toggle-expand.png) no-repeat; +} .icon-button.cross-circle { background: transparent url(../images/fugue/cross-circle-bw.png) no-repeat;margin-right:0px; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for BWA -R option.
by Bitbucket 10 Apr '12

10 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e5182b8038e8/ changeset: e5182b8038e8 user: dan date: 2012-04-10 15:24:25 summary: Fix for BWA -R option. affected #: 3 files diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.1"> +<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2"><description></description><parallelism method="basic"></parallelism><command interpreter="python"> @@ -42,7 +42,7 @@ --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign=$params.suboptAlign + --suboptAlign="${params.suboptAlign}" --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --outputTopNDisc=$params.outputTopNDisc @@ -125,7 +125,7 @@ <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> @@ -249,7 +249,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> @@ -300,7 +300,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py +++ b/tools/sr_mapping/bwa_wrapper.py @@ -54,7 +54,7 @@ parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' ) parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' ) parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' ) - parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' ) + parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', default=None, help='Proceed with suboptimal alignments even if the top hit is a repeat' ) parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' ) parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' ) parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' ) @@ -182,8 +182,8 @@ seed = '-l %s' % options.seed else: seed = '' - if options.suboptAlign == 'true': - suboptAlign = '-R' + if options.suboptAlign: + suboptAlign = '-R "%s"' % ( options.suboptAlign ) else: suboptAlign = '' if options.noIterSearch == 'true': diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2"> +<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3"><description></description><parallelism method="basic"></parallelism><command interpreter="python"> @@ -45,7 +45,7 @@ --mismatchPenalty=$params.mismatchPenalty --gapOpenPenalty=$params.gapOpenPenalty --gapExtensPenalty=$params.gapExtensPenalty - --suboptAlign=$params.suboptAlign + --suboptAlign="${params.suboptAlign}" --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN --outputTopNDisc=$params.outputTopNDisc @@ -122,7 +122,7 @@ <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> @@ -226,7 +226,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> @@ -263,7 +263,7 @@ <param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" /> - <param name="suboptAlign" value="true" /> + <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Do not add hidden tools to the tool panel.
by Bitbucket 09 Apr '12

09 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7f78b2bf339f/ changeset: 7f78b2bf339f user: dan date: 2012-04-10 05:24:31 summary: Do not add hidden tools to the tool panel. affected #: 1 file diff -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -490,52 +490,57 @@ def to_dict( self, trans, in_panel=True, trackster=False ): - def filter_for_trackster( item ): + def filter_for_panel( item, filters ): """ Filters tool panel elements so that only those that are compatible - with Trackster are kept. + with provided filters are kept. """ - + def _apply_filter( filter_item, filter_list ): + for filter_method in filter_list: + if not filter_method( filter_item ): + return False + return True if isinstance( item, Tool ): - # If tool has a trackster config, it can be used in Trackster. - if tool.trackster_conf: + if _apply_filter( item, filters[ 'tool' ] ): return item elif isinstance( item, ToolSectionLabel ): - # Tool label cannot be directly filtered. - return item + if _apply_filter( item, filters[ 'label' ] ): + return item elif isinstance( item, ToolSection ): # Filter section item-by-item. Only show a label if there are - # trackster-compatible tools below it. - cur_label_key = None - tools_under_label = False - filtered_elems = item.elems.copy() - for key, section_item in item.elems.items(): - if isinstance( section_item, Tool ): - # Filter tool. - if section_item.trackster_conf: - tools_under_label = True - else: - del filtered_elems[ key ] - elif isinstance( section_item, ToolSectionLabel ): - # If there is a label and it does not have tools, - # remove it. - if cur_label_key and not tools_under_label: - del filtered_elems[ cur_label_key ] + # non-filtered tools below it. + + if _apply_filter( item, filters[ 'section' ] ): + cur_label_key = None + tools_under_label = False + filtered_elems = item.elems.copy() + for key, section_item in item.elems.items(): + if isinstance( section_item, Tool ): + # Filter tool. + if _apply_filter( section_item, filters[ 'tool' ] ): + tools_under_label = True + else: + del filtered_elems[ key ] + elif isinstance( section_item, ToolSectionLabel ): + # If there is a label and it does not have tools, + # remove it. + if ( cur_label_key and not tools_under_label ) or not _apply_filter( section_item, filters[ 'label' ] ): + del filtered_elems[ cur_label_key ] - # Reset attributes for new label. - cur_label_key = key - tools_under_label = False - - - # Handle last label. - if cur_label_key and not tools_under_label: - del filtered_elems[ cur_label_key ] - - # Only return section if there are elements. - if len( filtered_elems ) != 0: - copy = item.copy() - copy.elems = filtered_elems - return copy + # Reset attributes for new label. + cur_label_key = key + tools_under_label = False + + + # Handle last label. + if cur_label_key and not tools_under_label: + del filtered_elems[ cur_label_key ] + + # Only return section if there are elements. + if len( filtered_elems ) != 0: + copy = item.copy() + copy.elems = filtered_elems + return copy return None @@ -547,13 +552,15 @@ panel_elts = [ val for val in self.tool_panel.itervalues() ] # Filter if necessary. + filters = dict( tool=[ lambda x: not x._is_hidden_for_user( trans.user ) ], section=[], label=[] ) #hidden tools filter if trackster: - filtered_panel_elts = [] - for index, elt in enumerate( panel_elts ): - elt = filter_for_trackster( elt ) - if elt: - filtered_panel_elts.append( elt ) - panel_elts = filtered_panel_elts + filters[ 'tool' ].append( lambda x: x.trackster_conf ) # If tool has a trackster config, it can be used in Trackster. + filtered_panel_elts = [] + for index, elt in enumerate( panel_elts ): + elt = filter_for_panel( elt, filters ) + if elt: + filtered_panel_elts.append( elt ) + panel_elts = filtered_panel_elts # Produce panel. rval = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: remove Genome Diversity {test, tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository
by Bitbucket 09 Apr '12

09 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0ffa2695e436/ changeset: 0ffa2695e436 user: richard_burhans date: 2012-04-09 22:34:51 summary: remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository affected #: 10 files diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_flanking_dna.txt --- a/test-data/gd.extract_flanking_dna.txt +++ /dev/null @@ -1,40 +0,0 @@ -SEQUENCE_ID=chr18_57379354_57380496 315 C T -SEQUENCE_TEMPLATE=CTCTCTGATGAGCAAGGAGCAGCTCTGATTGGGATCGCCAAGGAGCTGGAATCGGCCCTGGGTGTCTGTGTCCACGTCCTGACCTGGCTTGTTGGTGGCCACTGGCAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACTCCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCACCATCACAAACTCCTGCATCTGCAGCTTGAATGAGTCCAGAGCCTGAGACCCTATGAGGGAGACAGAGGTTCAAGCTGCAAGCCCAGCCCAGACCACCCCCCCCAGCCCCCGGGCCCCTCCTGGCCACCCCCTTCCACTCACCGCCCCACAGCATGGCCAAGAACAGTGGCAGGAACA -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr18_48070585_48071386 514 C T -SEQUENCE_TEMPLATE=GCCCTCCCCTGCCCAGTCCCTCAGCCCCTGCCTCCTCGTGCAGGCAGGCCTCCAGGATCTGCAGGCCAGACCTCCAGAAGGCCTTGTTCATGGCATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCACCCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTCTTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCCTGGGGAGACAGAGGTAGGAAGTGCCTTTGATGACCCTGAATATGGGGCACAGCACCTTCAAGAGCAGAGGGTACACATCTCAGTTGACACTAGGTTGGGGGACACACGCCTATGAGAGGCCTTGGTTT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr14_80021455_80022064 138 G A -SEQUENCE_TEMPLATE=ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG -SEQUENCE_TARGET=133,11 -= -SEQUENCE_ID=chr19_39866997_39874915 3117 C T -SEQUENCE_TEMPLATE=CCCAGCCAGAGAGGCCCTGGGGGCTGCGGCTACTCTGGCCCCCTTCCTTGCCTGAACAGTGCTTTGCTGGCCCCCGGGAGCCAGAGGGCACAGTCTCTTGGTGGTAGAGGAGGCCTGTGGCAAGGAAGCAGGCTCCGGGGGTGTCTCTTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAGCGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGCTGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTTGAGGAAGCCTGTGAGGGGTGGGATGGTGGGTGGTGGATAGAGCCCCGGGCTTGGCAGAAGCACACTCTCCCCTACCATCCCTAG -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr15_64470252_64471048 89 G A -SEQUENCE_TEMPLATE=TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT -SEQUENCE_TARGET=84,11 -= -SEQUENCE_ID=chr18_50154905_50155664 304 A G -SEQUENCE_TEMPLATE=GGTACCTTGGTTTCTCTGTCAAGAGACCTATGTGTTGACTGTCATCACTGTACCATGGTCGGGGGGTGGTCGGGAGGAGCCAGATGTGGGTCTGAATGAACATGTGGCGTTCTTGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAGTGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGCACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCGCCTCAGTCCTCCTCATCCATCCCTCCCGGGTCCCGTGGTGCTGGGGGATGGGTCCTCCCAGGCTGCCTCCCCTCTGAGGGGCTCTTCCCCCACACAGGGCCGGGCATTT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr2_75111355_75112576 314 A C -SEQUENCE_TEMPLATE=TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr8_93901796_93905612 2471 A C -SEQUENCE_TEMPLATE=GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr10_7434473_7435447 524 T C -SEQUENCE_TEMPLATE=ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC -SEQUENCE_TARGET=196,11 -= -SEQUENCE_ID=chr19_14240610_14242055 232 C T -SEQUENCE_TEMPLATE=CAACATTGTAAAGTAATTATACTCCAATTAAAAAACACAGTGATATCAAAGATGATTTCCAATACTAAAATCTATCTCCAAGAATTTACAGCTTTGAAGAAAATTTTACAATCTCCGGAATTCATGTTAATATTGAAACAACATTTCTGTCCTAATTATTTATTGGAACCTCTTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGACGGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACTTTCGGAGAGGAAAACAGGAAGAGGATGACCAATAGCTATTTGAAAAGAGCTGAGAACTCTAGAATCACCCAAGCGACGTGTGCACTGTTAAATTCTGGAGGGGGTTTGATCAAAGCGGAGATTG -SEQUENCE_TARGET=196,11 -= diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_primers.txt --- a/test-data/gd.extract_primers.txt +++ /dev/null @@ -1,119 +0,0 @@ -> chr18_57379354_57380496 315 C T 0.014036 - BanI - 1 CAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACT - >>>>>>>>>>>>>>>>>>>> - - 61 CCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCAC - - -121 CATCACAAACTCCTGCATCTGCAGC - <<<<<<<<<<<<<<<<<<<< - -> chr18_48070585_48071386 514 C T 0.163186 - - 1 ATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCAC - >>>>>>>>>>>>>>>>>>>> - - 61 CCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTC - - -121 TTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCC - <<<<< - -181 TGGGGAGACAGAGGTAGG - <<<<<<<<<<<<<<< - -> chr14_80021455_80022064 138 G A 0.194886 - Hsp92II - 1 CGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCT - >>>>>>>>>>>>>>>>>>>> - - 61 TGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGC - <<<<<<<<<<<<< - -121 GTAGTGCAAA - <<<<<<< - -> chr19_39866997_39874915 3117 C T 0.946156 - BstOI - 1 TTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAG - >>>>>>>>>>>>>>>>>>>> - - 61 CGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGC - - -121 TGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTT - <<<<<<<<<<<<<<<<<<<< - -> chr15_64470252_64471048 89 G A 1.325099 - - 1 GTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTC - >>>>>>>>>>>>>>>>>>>> - - 61 AGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGG - - -121 GCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGAT - <<<<<< - -181 GCATCGCTCTCTTCCAC - <<<<<<<<<<<<<< - -> chr18_50154905_50155664 304 A G 0.578070 - - 1 TGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAG - >>>>>>>>>>>>>>>>>>>> - - 61 TGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGC - - -121 ACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCG - - -181 CCTCAGTCCTCCTCATCCATCCCTC - <<<<<<<<<<<<<<<<<<<< - -> chr2_75111355_75112576 314 A C 0.613831 - - 1 TTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGC - >>>>>>>>>>>>>>>>>>>> - - 61 AAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAA - - -121 CAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACAT - - -181 GATCAGGGGCAAGTTCTATTGGATA - <<<<<<<<<<<<<<<<<<<< - -> chr8_93901796_93905612 2471 A C 0.322555 - MboI,Sau3AI - 1 GGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATn - >>>>>>>>>>>>>>>>>>>> - - 61 GCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAG - <<<<<<<<<<<<<<<<<<<< - -121 C - - -> chr10_7434473_7435447 524 T C 1.119264 - - 1 CCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACA - >>>>>>>>>>>>>>>>>>>> - - 61 AATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGA - - -121 CAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAAT - <<<<<<<<<<<<<<<<<<<< - -> chr19_14240610_14242055 232 C T 0.835026 - - 1 TTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGAC - >>>>>>>>>>>>>>>>>>>> - - 61 GGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACT - <<<<<<<<<<<<<<<<<<<< - diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.sample.wsf --- a/test-data/gd.sample.wsf +++ /dev/null @@ -1,12 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 -chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 -chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 -chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 -chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 -chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0 -chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0 -chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 -chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 -chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_restriction_enzymes.wsf --- a/test-data/gd.select_restriction_enzymes.wsf +++ /dev/null @@ -1,5 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1 -chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1 -chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_snps.wsf --- a/test-data/gd.select_snps.wsf +++ /dev/null @@ -1,7 +0,0 @@ -#species=bighorn -#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP -chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0 -chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0 -chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2 -chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0 -chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0 diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ /dev/null @@ -1,22 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of sequence length files. You will need to create these -# sequence length files and then create a gd.chrlens.loc file similar to -# this one (store it in this directory) that points to the directories -# in which these sequence length files are stored. The gd.chrlens.loc -# file has the following format (white space characters are TAB -# characters): -# -#<species><reference_species_file_path> -# -# So, for example, if you used Monodelphis domestica as the reference -# species for a collection of Sarcophilus harrisii SNPs, then the -# gd.chrlens.loc entry would look like this: -# -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt -# -# Your gd.chrlens.loc file should include an entry for each pair of -# species SNPs and reference species. For example: -# -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ /dev/null @@ -1,22 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of primers files. You will need to create these primers -# files and then create a gd.primers.loc file similar to this one (store -# it in this directory) that points to the directories in which these -# primers files are stored. The gd.primers.loc file has the following -# format (white space characters are TAB characters): -# -#<species><primers_file_path> -# -# So, for example, if you had a primers file located at -# /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of -# Ovis canadensis SNPs, then the gd.primers.loc entry would look like -# this: -# -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -# -# Your gd.primers.loc file should include an entry for each pair of -# species SNPs and primers file. For example: -# -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.restriction_enzymes.txt.sample --- a/tool-data/gd.restriction_enzymes.txt.sample +++ /dev/null @@ -1,99 +0,0 @@ -Acc65I - GGTACC Acc65I -AccB7I - CCANNNNNTGG AccB7I -AccI - GT(A/C)(G/T)AC AccI -AccIII - TCCGGA AccIII -AcyI - G(A/G)CG(C/T)C AcyI -AgeI - ACCGGT AgeI -AluI - AGCT AluI -Alw44I - GTGCAC Alw44I -ApaI - GGGCCC ApaI -AvaI - C(C/T)CG(A/G)G AvaI -AvaII - GG(A/T)CC AvaII -BalI - TGGCCA BalI -BamHI - GGATCC BamHI -BanI - GG(C/T)(A/G)CC BanI -BanII - G(A/G)GC(C/T)C BanII -BbuI - GCATGC BbuI -BclI - TGATCA BclI -BglI - GCCNNNNNGGC BglI -BglII - AGATCT BglII -BsaMI - GAATGC BsaMI -BsaOI - CG(A/G)(C/T)CG BsaOI -Bsp1286I - G(A/G/T)GC(A/C/T)C Bsp1286I -BsrBRI - GATNNNNATC BsrBRI -BsrSI - ACTGG BsrSI -BssHII - GCGCGC BssHII -Bst98I - CTTAAG Bst98I -BstEII - GGTNACC BstEII -BstOI - CC(A/T)GG BstOI -BstXI - CCANNNNNNTGG BstXI -BstZI - CGGCCG BstZI -Bsu36I - CCTNAGG Bsu36I -CfoI - GCGC CfoI -ClaI - ATCGAT ClaI -Csp45I - TTCGAA Csp45I -CspI - CGG(A/T)CCG CspI -DdeI - CTNAG DdeI -DpnI - GATC DpnI -DraI - TTTAAA DraI -EclHKI - GACNNNNNGTC EclHKI -Eco47III - AGCGCT Eco47III -Eco52I - CGGCCG Eco52I -Eco72I - CACGTG Eco72I -EcoRI - GAATTC EcoRI -EcoRV - GATATC EcoRV -HaeII - (A/G)GCGC(C/T) HaeII -HaeIII - GGCC HaeIII -HhaI - GCGC HhaI -HincII - GT(C/T)(A/G)AC HincII -HindIII - AAGCTT HindIII -HinfI - GANTC HinfI -HpaI - GTTAAC HpaI -HpaII - CCGG HpaII -Hsp92I - G(A/G)CG(C/T)C Hsp92I -Hsp92II - CATG Hsp92II -I-PpoI - TAACTATGACTCTCTTAAGGTAGCCAAAT I-PpoI -KpnI - GGTACC KpnI -MboI - GATC MboI -MluI - ACGCGT MluI -MspA1I - C(A/C)GC(G/T)G MspA1I -MspI - CCGG MspI -NaeI - GCCGGC NaeI -NarI - GGCGCC NarI -NciI - CC(C/G)GG NciI -NcoI - CCATGG NcoI -NdeI - CATATG NdeI -NgoMIV - GCCGGC NgoMIV -NheI - GCTAGC NheI -NotI - GCGGCCGC NotI -NruI - TCGCGA NruI -NsiI - ATGCAT NsiI -PstI - CTGCAG PstI -PvuI - CGATCG PvuI -PvuII - CAGCTG PvuII -RsaI - GTAC RsaI -SacI - GAGCTC SacI -SacII - CCGCGG SacII -SalI - GTCGAC SalI -Sau3AI - GATC Sau3AI -Sau96I - GGNCC Sau96I -ScaI - AGTACT ScaI -SfiI - GGCCNNNNNGGCC SfiI -SgfI - GCGATCGC SgfI -SinI - GG(A/T)CC SinI -SmaI - CCCGGG SmaI -SnaBI - TACGTA SnaBI -SpeI - ACTAGT SpeI -SphI - GCATGC SphI -SspI - AATATT SspI -StuI - AGGCCT StuI -StyI - CC(A/T)(A/T)GG StyI -TaqI - TCGA TaqI -Tru9I - TTAA Tru9I -Tth111I - GACNNNGTC Tth111I -VspI - ATTAAT VspI -XbaI - TCTAGA XbaI -XhoI - CTCGAG XhoI -XhoII - (A/G)GATC(C/T) XhoII -XmaI - CCCGGG XmaI -XmnI - GAANNNNTTC XmnI diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ /dev/null @@ -1,21 +0,0 @@ -# This is a sample file distributed with Galaxy that enables tools to -# use a directory of SNP call files. You will need to create these SNP -# call files and then create a gd.snps.loc file similar to this one (store -# it in this directory) that points to the directories in which these -# SNP call files are stored. The gd.snps.loc file has the following -# format (white space characters are TAB characters): -# -#<species><SNP_call_file_path> -# -# So, for example, if you had a SNP call file located at -# /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of -# Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: -# -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -# -# Your gd.snps.loc file should include an entry for each pair of species -# SNPs and SNP call file. For example: -# -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt -#...etc... diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.species.txt.sample --- a/tool-data/gd.species.txt.sample +++ /dev/null @@ -1,3 +0,0 @@ -# genome diversity species -tasmanian_devil Tasmanian devil -bighorn bighorn Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Comment out recently used tool update for now because it is not implemented yet.
by Bitbucket 09 Apr '12

09 Apr '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0edea146c964/ changeset: 0edea146c964 user: jgoecks date: 2012-04-09 22:17:46 summary: Comment out recently used tool update for now because it is not implemented yet. affected #: 1 file diff -r 507135da0b2c15ddbb05759c5d38a0ed0f429d0a -r 0edea146c96436e63076550c595bcc444ba2cdb0 templates/tool_executed.mako --- a/templates/tool_executed.mako +++ b/templates/tool_executed.mako @@ -16,7 +16,7 @@ %if trans.user: if (inside_galaxy_frameset) { - parent.frames.galaxy_tools.update_recently_used(); + //parent.frames.galaxy_tools.update_recently_used(); } %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 09 Apr '12

09 Apr '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fe54618dbd31/ changeset: fe54618dbd31 user: jgoecks date: 2012-04-09 21:58:25 summary: Tool menu changes: (a) enable Toolbox to be directly dictified; and (b) enable Toolbox to return only tools compatible with Trackster. affected #: 3 files diff -r 7274516136812ee0a84aa69f420348848d1b5b08 -r fe54618dbd317fc1c8e9d8fd2f1650717878eade lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -487,18 +487,106 @@ Returns a SQLAlchemy session """ return self.app.model.context + + def to_dict( self, trans, in_panel=True, trackster=False ): + + def filter_for_trackster( item ): + """ + Filters tool panel elements so that only those that are compatible + with Trackster are kept. + """ + + if isinstance( item, Tool ): + # If tool has a trackster config, it can be used in Trackster. + if tool.trackster_conf: + return item + elif isinstance( item, ToolSectionLabel ): + # Tool label cannot be directly filtered. + return item + elif isinstance( item, ToolSection ): + # Filter section item-by-item. Only show a label if there are + # trackster-compatible tools below it. + cur_label_key = None + tools_under_label = False + filtered_elems = item.elems.copy() + for key, section_item in item.elems.items(): + if isinstance( section_item, Tool ): + # Filter tool. + if section_item.trackster_conf: + tools_under_label = True + else: + del filtered_elems[ key ] + elif isinstance( section_item, ToolSectionLabel ): + # If there is a label and it does not have tools, + # remove it. + if cur_label_key and not tools_under_label: + del filtered_elems[ cur_label_key ] + + # Reset attributes for new label. + cur_label_key = key + tools_under_label = False + + + # Handle last label. + if cur_label_key and not tools_under_label: + del filtered_elems[ cur_label_key ] + + # Only return section if there are elements. + if len( filtered_elems ) != 0: + copy = item.copy() + copy.elems = filtered_elems + return copy + + return None + + # + # Dictify toolbox. + # + + if in_panel: + panel_elts = [ val for val in self.tool_panel.itervalues() ] + + # Filter if necessary. + if trackster: + filtered_panel_elts = [] + for index, elt in enumerate( panel_elts ): + elt = filter_for_trackster( elt ) + if elt: + filtered_panel_elts.append( elt ) + panel_elts = filtered_panel_elts + + # Produce panel. + rval = [] + for elt in panel_elts: + rval.append( elt.to_dict( trans ) ) + else: + tools = [] + for id, tool in self.app.toolbox.tools_by_id.items(): + tools.append( tool.to_dict( trans ) ) + rval = tools + + return rval class ToolSection( object ): """ A group of tools with similar type/purpose that will be displayed as a group in the user interface. """ - def __init__( self, elem ): - self.name = elem.get( "name" ) - self.id = elem.get( "id" ) - self.version = elem.get( "version" ) or '' + def __init__( self, elem=None ): + f = lambda elem, val: elem is not None and elem.get( val ) or '' + self.name = f( elem, 'name' ) + self.id = f( elem, 'id' ) + self.version = f( elem, 'version' ) self.elems = odict() + def copy( self ): + copy = ToolSection() + copy.name = self.name + copy.id = self.id + copy.version = self.version + copy.elems = self.elems.copy() + return copy + def to_dict( self, trans ): """ Return a dict that includes section's attributes. """ section_elts = [] @@ -880,7 +968,7 @@ self.is_workflow_compatible = self.check_workflow_compatible() # Trackster configuration. trackster_conf = root.find( "trackster_conf" ) - if trackster_conf: + if trackster_conf is not None: self.trackster_conf = TracksterConfig.parse( trackster_conf ) else: self.trackster_conf = None diff -r 7274516136812ee0a84aa69f420348848d1b5b08 -r fe54618dbd317fc1c8e9d8fd2f1650717878eade lib/galaxy/web/controllers/tools.py --- a/lib/galaxy/web/controllers/tools.py +++ b/lib/galaxy/web/controllers/tools.py @@ -14,18 +14,13 @@ GET /api/tools: returns a list of tools defined by parameters parameters: in_panel - if true, tools are returned in panel structure, including sections and labels + trackster - if true, only tools that are compatible with Trackster are returned """ + + # Read params. in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) - if in_panel: - panel_elts = [] - for key, val in self.app.toolbox.tool_panel.items(): - panel_elts.append( val.to_dict( trans ) ) - rval = panel_elts - else: - tools = [] - for id, tool in self.app.toolbox.tools_by_id.items(): - tools.append( tool.to_dict( trans ) ) - rval = tools - - return rval + trackster = util.string_as_bool( kwds.get( 'trackster', 'False' ) ) + + # Create return value. + return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) \ No newline at end of file diff -r 7274516136812ee0a84aa69f420348848d1b5b08 -r fe54618dbd317fc1c8e9d8fd2f1650717878eade templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -25,9 +25,7 @@ if trans.user and trans.user.preferences.get( "show_tool_search", "False" ) == "False": tool_search_hidden = "true" - dictified_panel = [] - for key, val in trans.app.toolbox.tool_panel.items(): - dictified_panel.append( val.to_dict( trans ) ) + dictified_panel = trans.app.toolbox.to_dict( trans ) %><script type="text/javascript"> https://bitbucket.org/galaxy/galaxy-central/changeset/507135da0b2c/ changeset: 507135da0b2c user: jgoecks date: 2012-04-09 21:59:45 summary: Merge affected #: 1 file diff -r fe54618dbd317fc1c8e9d8fd2f1650717878eade -r 507135da0b2c15ddbb05759c5d38a0ed0f429d0a lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -141,7 +141,7 @@ if hasattr( imported_module, datatype_class_name ): datatype_class = getattr( imported_module, datatype_class_name ) except Exception, e: - full_path = os.path.join( full_path, proprietary_datatype_module ) + full_path = os.path.join( proprietary_path, proprietary_datatype_module ) self.log.debug( "Exception importing proprietary code file %s: %s" % ( str( full_path ), str( e ) ) ) finally: lock.release() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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