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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> 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 @@ <!-- Do nothing here --></when><when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree <pedigree>"> + <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" help="-pedString,--pedigreeString <pedigreeString>"> + <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" 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 <pedigreeValidationType>"><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 <read_filter>"><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 <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" help="-XL,--excludeIntervals <excludeIntervals>"> + <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" help="-isr,--interval_set_rule <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="-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 <downsampling_type>"><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 <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>"/> + <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> @@ -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 <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>"/> + <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" help="-baq,--baq <baq>"> + <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. -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 <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>"> + <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><!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></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 <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" 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 <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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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