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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -327,20 +327,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -355,10 +355,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -369,34 +369,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/depth_of_coverage.xml
--- a/tools/gatk/depth_of_coverage.xml
+++ b/tools/gatk/depth_of_coverage.xml
@@ -239,17 +239,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -351,20 +351,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -379,10 +379,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -393,34 +393,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/indel_realigner.xml
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -179,17 +179,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -291,20 +291,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -319,10 +319,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -333,34 +333,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/print_reads.xml
--- a/tools/gatk/print_reads.xml
+++ b/tools/gatk/print_reads.xml
@@ -147,17 +147,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -259,20 +259,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -287,10 +287,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -301,34 +301,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/realigner_target_creator.xml
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -165,17 +165,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -277,20 +277,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -305,10 +305,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -319,34 +319,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/table_recalibration.xml
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -154,17 +154,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -266,20 +266,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -294,10 +294,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -308,34 +308,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -220,17 +220,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -332,20 +332,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -360,10 +360,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -374,34 +374,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_annotator.xml
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -245,17 +245,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -357,20 +357,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -385,10 +385,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -399,34 +399,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_apply_recalibration.xml
--- a/tools/gatk/variant_apply_recalibration.xml
+++ b/tools/gatk/variant_apply_recalibration.xml
@@ -135,17 +135,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -247,20 +247,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -275,10 +275,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -289,34 +289,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_combine.xml
--- a/tools/gatk/variant_combine.xml
+++ b/tools/gatk/variant_combine.xml
@@ -155,17 +155,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -267,20 +267,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -295,10 +295,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -309,34 +309,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_eval.xml
--- a/tools/gatk/variant_eval.xml
+++ b/tools/gatk/variant_eval.xml
@@ -211,17 +211,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -323,20 +323,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -351,10 +351,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -365,34 +365,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_filtration.xml
--- a/tools/gatk/variant_filtration.xml
+++ b/tools/gatk/variant_filtration.xml
@@ -164,17 +164,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -276,20 +276,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -304,10 +304,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -318,34 +318,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_recalibrator.xml
--- a/tools/gatk/variant_recalibrator.xml
+++ b/tools/gatk/variant_recalibrator.xml
@@ -370,17 +370,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -482,20 +482,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -510,10 +510,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -524,34 +524,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variant_select.xml
--- a/tools/gatk/variant_select.xml
+++ b/tools/gatk/variant_select.xml
@@ -209,17 +209,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -321,20 +321,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -349,10 +349,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -363,34 +363,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
diff -r bc94cf3ea6d037eeb42e6875d142d712cd87a7ff -r 99b2fe57e16790a413f6d76deaf5b44a7c77e992 tools/gatk/variants_validate.xml
--- a/tools/gatk/variants_validate.xml
+++ b/tools/gatk/variants_validate.xml
@@ -135,17 +135,17 @@
<!-- 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 &lt;pedigree&gt;"><param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/></repeat>
- <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString <pedigreeString>">
+ <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"><param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/></repeat>
- <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType <pedigreeValidationType>">
+ <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &lt;pedigreeValidationType&gt;"><option value="STRICT" selected="True">STRICT</option><option value="SILENT">SILENT</option></param>
- <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter <read_filter>">
+ <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &lt;read_filter&gt;"><conditional name="read_filter_type"><param name="read_filter_type_selector" type="select" label="Read Filter Type"><option value="BadCigar">BadCigar</option>
@@ -247,20 +247,20 @@
</when></conditional></repeat>
- <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals <intervals>">
+ <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"><param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals <excludeIntervals>">
+ <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"><param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /></repeat>
- <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule <interval_set_rule>">
+ <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param><conditional name="downsampling_type">
- <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type <downsampling_type>">
+ <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &lt;downsampling_type&gt;"><option value="NONE" selected="True">NONE</option><option value="ALL_READS">ALL_READS</option><option value="BY_SAMPLE">BY_SAMPLE</option>
@@ -275,10 +275,10 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when>
@@ -289,34 +289,34 @@
<option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction">
- <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction <downsample_to_fraction>"/>
+ <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &lt;downsample_to_fraction&gt;"/></when><when value="downsample_to_coverage">
- <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage <downsample_to_coverage>"/>
+ <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &lt;downsample_to_coverage&gt;"/></when></conditional></when></conditional>
- <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq <baq>">
+ <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &lt;baq&gt;"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param>
- <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty>" />
+ <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &lt;baqGapOpenPenalty&gt;" /><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
- <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities <defaultBaseQualities>"/>
- <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness <validation_strictness>">
+ <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &lt;defaultBaseQualities&gt;"/>
+ <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &lt;validation_strictness&gt;"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option><!-- <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 &lt;interval_merging&gt;"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param>
- <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list <read_group_black_list>">
+ <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"><conditional name="read_group_black_list_type"><param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"><option value="file" selected="True">Filters in file</option>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e5182b8038e8/
changeset: e5182b8038e8
user: dan
date: 2012-04-10 15:24:25
summary: Fix for BWA -R option.
affected #: 3 files
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_color_wrapper.xml
--- a/tools/sr_mapping/bwa_color_wrapper.xml
+++ b/tools/sr_mapping/bwa_color_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.1">
+<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2"><description></description><parallelism method="basic"></parallelism><command interpreter="python">
@@ -42,7 +42,7 @@
--mismatchPenalty=$params.mismatchPenalty
--gapOpenPenalty=$params.gapOpenPenalty
--gapExtensPenalty=$params.gapExtensPenalty
- --suboptAlign=$params.suboptAlign
+ --suboptAlign="${params.suboptAlign}"
--noIterSearch=$params.noIterSearch
--outputTopN=$params.outputTopN
--outputTopNDisc=$params.outputTopNDisc
@@ -125,7 +125,7 @@
<param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
- <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
+ <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" />
@@ -249,7 +249,7 @@
<param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" />
- <param name="suboptAlign" value="true" />
+ <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
@@ -300,7 +300,7 @@
<param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" />
- <param name="suboptAlign" value="true" />
+ <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.py
--- a/tools/sr_mapping/bwa_wrapper.py
+++ b/tools/sr_mapping/bwa_wrapper.py
@@ -54,7 +54,7 @@
parser.add_option( '-M', '--mismatchPenalty', dest='mismatchPenalty', help='Mismatch penalty' )
parser.add_option( '-O', '--gapOpenPenalty', dest='gapOpenPenalty', help='Gap open penalty' )
parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' )
- parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' )
+ parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', default=None, help='Proceed with suboptimal alignments even if the top hit is a repeat' )
parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' )
parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' )
parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' )
@@ -182,8 +182,8 @@
seed = '-l %s' % options.seed
else:
seed = ''
- if options.suboptAlign == 'true':
- suboptAlign = '-R'
+ if options.suboptAlign:
+ suboptAlign = '-R "%s"' % ( options.suboptAlign )
else:
suboptAlign = ''
if options.noIterSearch == 'true':
diff -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 -r e5182b8038e8618529594dea85bc3f304e51a11c tools/sr_mapping/bwa_wrapper.xml
--- a/tools/sr_mapping/bwa_wrapper.xml
+++ b/tools/sr_mapping/bwa_wrapper.xml
@@ -1,4 +1,4 @@
-<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2">
+<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3"><description></description><parallelism method="basic"></parallelism><command interpreter="python">
@@ -45,7 +45,7 @@
--mismatchPenalty=$params.mismatchPenalty
--gapOpenPenalty=$params.gapOpenPenalty
--gapExtensPenalty=$params.gapExtensPenalty
- --suboptAlign=$params.suboptAlign
+ --suboptAlign="${params.suboptAlign}"
--noIterSearch=$params.noIterSearch
--outputTopN=$params.outputTopN
--outputTopNDisc=$params.outputTopNDisc
@@ -122,7 +122,7 @@
<param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /><param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /><param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" />
- <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" />
+ <param name="suboptAlign" type="integer" optional="True" label="Proceed with suboptimal alignments if there are no more than INT equally best hits. (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /><param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /><param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /><param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" />
@@ -226,7 +226,7 @@
<param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" />
- <param name="suboptAlign" value="true" />
+ <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
@@ -263,7 +263,7 @@
<param name="mismatchPenalty" value="3" /><param name="gapOpenPenalty" value="11" /><param name="gapExtensPenalty" value="4" />
- <param name="suboptAlign" value="true" />
+ <param name="suboptAlign" value="" /><param name="noIterSearch" value="true" /><param name="outputTopN" value="3" /><param name="outputTopNDisc" value="10" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/7f78b2bf339f/
changeset: 7f78b2bf339f
user: dan
date: 2012-04-10 05:24:31
summary: Do not add hidden tools to the tool panel.
affected #: 1 file
diff -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 -r 7f78b2bf339f24f57b686e7c4bdb1fe301e8ed12 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -490,52 +490,57 @@
def to_dict( self, trans, in_panel=True, trackster=False ):
- def filter_for_trackster( item ):
+ def filter_for_panel( item, filters ):
"""
Filters tool panel elements so that only those that are compatible
- with Trackster are kept.
+ with provided filters are kept.
"""
-
+ def _apply_filter( filter_item, filter_list ):
+ for filter_method in filter_list:
+ if not filter_method( filter_item ):
+ return False
+ return True
if isinstance( item, Tool ):
- # If tool has a trackster config, it can be used in Trackster.
- if tool.trackster_conf:
+ if _apply_filter( item, filters[ 'tool' ] ):
return item
elif isinstance( item, ToolSectionLabel ):
- # Tool label cannot be directly filtered.
- return item
+ if _apply_filter( item, filters[ 'label' ] ):
+ return item
elif isinstance( item, ToolSection ):
# Filter section item-by-item. Only show a label if there are
- # trackster-compatible tools below it.
- cur_label_key = None
- tools_under_label = False
- filtered_elems = item.elems.copy()
- for key, section_item in item.elems.items():
- if isinstance( section_item, Tool ):
- # Filter tool.
- if section_item.trackster_conf:
- tools_under_label = True
- else:
- del filtered_elems[ key ]
- elif isinstance( section_item, ToolSectionLabel ):
- # If there is a label and it does not have tools,
- # remove it.
- if cur_label_key and not tools_under_label:
- del filtered_elems[ cur_label_key ]
+ # non-filtered tools below it.
+
+ if _apply_filter( item, filters[ 'section' ] ):
+ cur_label_key = None
+ tools_under_label = False
+ filtered_elems = item.elems.copy()
+ for key, section_item in item.elems.items():
+ if isinstance( section_item, Tool ):
+ # Filter tool.
+ if _apply_filter( section_item, filters[ 'tool' ] ):
+ tools_under_label = True
+ else:
+ del filtered_elems[ key ]
+ elif isinstance( section_item, ToolSectionLabel ):
+ # If there is a label and it does not have tools,
+ # remove it.
+ if ( cur_label_key and not tools_under_label ) or not _apply_filter( section_item, filters[ 'label' ] ):
+ del filtered_elems[ cur_label_key ]
- # Reset attributes for new label.
- cur_label_key = key
- tools_under_label = False
-
-
- # Handle last label.
- if cur_label_key and not tools_under_label:
- del filtered_elems[ cur_label_key ]
-
- # Only return section if there are elements.
- if len( filtered_elems ) != 0:
- copy = item.copy()
- copy.elems = filtered_elems
- return copy
+ # Reset attributes for new label.
+ cur_label_key = key
+ tools_under_label = False
+
+
+ # Handle last label.
+ if cur_label_key and not tools_under_label:
+ del filtered_elems[ cur_label_key ]
+
+ # Only return section if there are elements.
+ if len( filtered_elems ) != 0:
+ copy = item.copy()
+ copy.elems = filtered_elems
+ return copy
return None
@@ -547,13 +552,15 @@
panel_elts = [ val for val in self.tool_panel.itervalues() ]
# Filter if necessary.
+ filters = dict( tool=[ lambda x: not x._is_hidden_for_user( trans.user ) ], section=[], label=[] ) #hidden tools filter
if trackster:
- filtered_panel_elts = []
- for index, elt in enumerate( panel_elts ):
- elt = filter_for_trackster( elt )
- if elt:
- filtered_panel_elts.append( elt )
- panel_elts = filtered_panel_elts
+ filters[ 'tool' ].append( lambda x: x.trackster_conf ) # If tool has a trackster config, it can be used in Trackster.
+ filtered_panel_elts = []
+ for index, elt in enumerate( panel_elts ):
+ elt = filter_for_panel( elt, filters )
+ if elt:
+ filtered_panel_elts.append( elt )
+ panel_elts = filtered_panel_elts
# Produce panel.
rval = []
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0ffa2695e436/
changeset: 0ffa2695e436
user: richard_burhans
date: 2012-04-09 22:34:51
summary: remove Genome Diversity {test,tool}-data from galaxy-central. this is now in the genome_diversity toolshed repository
affected #: 10 files
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_flanking_dna.txt
--- a/test-data/gd.extract_flanking_dna.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-SEQUENCE_ID=chr18_57379354_57380496 315 C T
-SEQUENCE_TEMPLATE=CTCTCTGATGAGCAAGGAGCAGCTCTGATTGGGATCGCCAAGGAGCTGGAATCGGCCCTGGGTGTCTGTGTCCACGTCCTGACCTGGCTTGTTGGTGGCCACTGGCAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACTCCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCACCATCACAAACTCCTGCATCTGCAGCTTGAATGAGTCCAGAGCCTGAGACCCTATGAGGGAGACAGAGGTTCAAGCTGCAAGCCCAGCCCAGACCACCCCCCCCAGCCCCCGGGCCCCTCCTGGCCACCCCCTTCCACTCACCGCCCCACAGCATGGCCAAGAACAGTGGCAGGAACA
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr18_48070585_48071386 514 C T
-SEQUENCE_TEMPLATE=GCCCTCCCCTGCCCAGTCCCTCAGCCCCTGCCTCCTCGTGCAGGCAGGCCTCCAGGATCTGCAGGCCAGACCTCCAGAAGGCCTTGTTCATGGCATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCACCCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTCTTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCCTGGGGAGACAGAGGTAGGAAGTGCCTTTGATGACCCTGAATATGGGGCACAGCACCTTCAAGAGCAGAGGGTACACATCTCAGTTGACACTAGGTTGGGGGACACACGCCTATGAGAGGCCTTGGTTT
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr14_80021455_80022064 138 G A
-SEQUENCE_TEMPLATE=ACCCAGGGATCAAACCCAGGTCTCCCGCATTGCAGGCGGATTCTTTACTGTCTGAGCCTCCAGGGAAGCCCTCGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCTTGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGCGTAGTGCAAACGTTTGGGAAGGTGCTGTTTCAAGTAAGGCTTAAAGTGCTGGTCTGGTTTTTTACACTGAAATATAAATGGACATTGGATTTTGCAATGGAGAGTCTTCTAGAAGAGTCCAAGACATTCTCTCCAGAAAGCTGAAGG
-SEQUENCE_TARGET=133,11
-=
-SEQUENCE_ID=chr19_39866997_39874915 3117 C T
-SEQUENCE_TEMPLATE=CCCAGCCAGAGAGGCCCTGGGGGCTGCGGCTACTCTGGCCCCCTTCCTTGCCTGAACAGTGCTTTGCTGGCCCCCGGGAGCCAGAGGGCACAGTCTCTTGGTGGTAGAGGAGGCCTGTGGCAAGGAAGCAGGCTCCGGGGGTGTCTCTTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAGCGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGCTGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTTGAGGAAGCCTGTGAGGGGTGGGATGGTGGGTGGTGGATAGAGCCCCGGGCTTGGCAGAAGCACACTCTCCCCTACCATCCCTAG
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr15_64470252_64471048 89 G A
-SEQUENCE_TEMPLATE=TGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTCAGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGGGCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGATGCATCGCTCTCTTCCACGCCCTCAGCCAGGATCTCCTCCAGGGACAGCACATCTGCTTTGGCCTGCTGTGGCTGAGTCAGGAGCTTCCTCAGGACGTTCCT
-SEQUENCE_TARGET=84,11
-=
-SEQUENCE_ID=chr18_50154905_50155664 304 A G
-SEQUENCE_TEMPLATE=GGTACCTTGGTTTCTCTGTCAAGAGACCTATGTGTTGACTGTCATCACTGTACCATGGTCGGGGGGTGGTCGGGAGGAGCCAGATGTGGGTCTGAATGAACATGTGGCGTTCTTGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAGTGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGCACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCGCCTCAGTCCTCCTCATCCATCCCTCCCGGGTCCCGTGGTGCTGGGGGATGGGTCCTCCCAGGCTGCCTCCCCTCTGAGGGGCTCTTCCCCCACACAGGGCCGGGCATTT
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr2_75111355_75112576 314 A C
-SEQUENCE_TEMPLATE=TATCTTCATTTTTATTATAGACTCTCTGAACCAATTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGCAAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAACAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACATGATCAGGGGCAAGTTCTATTGGATATAGTCTTCAAGCATCTTGATTTGACTGAGCGTGACTATTTTGGTTTGCAGTTGACTGACGATTCCACTGATAACCCAGTAAGTTTAAGCTGTTGTCTTTCATTGTCATTGCAATTTTTCTGTCTTTATACTAGGTCCTTTCTGATTTACATTGTTCACTGATT
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr8_93901796_93905612 2471 A C
-SEQUENCE_TEMPLATE=GCTGCCGCTGGATTTACTTCTGCTTGGGTCGAGAGCGGGCTGGATGGGTGAAGAGTGGGCTCCCCGGCCCCTGACCAGGCAGGTGCAGACAAGTCGGAAGAAGGCCCGCCGCATCTCCTTGCTGGCCAGCGTGTAGATGACGGGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATnGCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAGCAGGCGATGAACACGCTCACCACGATCACCACGGTCCGCAGCAGGGCCATGGACCGCTCTGAGTTGTGCGGGCTGGCCACCCTGCGGCTGCTGGACTTCACCAGGAAGTAGATGCGTGCGTACAGGATCACGATGGTCAC
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr10_7434473_7435447 524 T C
-SEQUENCE_TEMPLATE=ATTATTAACAGAAACATTTCTTTTTCATTACCCAGGGGTTACACTGGTCGTTGATGTTAATCAGTTTTTGGAGAAGGAGAAGCAAAGTGATATTTTGTCTGTTCTGAAGCCTGCCGTTGGTAATACAAATGACGTAATCCCTGAATGTGCTGACAGGTACCATGACGCCCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACAAATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGACAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAATTTTTTAGTGTTTCTTTTCCTTTTTTGTCTTTTGGAAATCTGTGATTAACTTGGTGGC
-SEQUENCE_TARGET=196,11
-=
-SEQUENCE_ID=chr19_14240610_14242055 232 C T
-SEQUENCE_TEMPLATE=CAACATTGTAAAGTAATTATACTCCAATTAAAAAACACAGTGATATCAAAGATGATTTCCAATACTAAAATCTATCTCCAAGAATTTACAGCTTTGAAGAAAATTTTACAATCTCCGGAATTCATGTTAATATTGAAACAACATTTCTGTCCTAATTATTTATTGGAACCTCTTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGACGGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACTTTCGGAGAGGAAAACAGGAAGAGGATGACCAATAGCTATTTGAAAAGAGCTGAGAACTCTAGAATCACCCAAGCGACGTGTGCACTGTTAAATTCTGGAGGGGGTTTGATCAAAGCGGAGATTG
-SEQUENCE_TARGET=196,11
-=
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.extract_primers.txt
--- a/test-data/gd.extract_primers.txt
+++ /dev/null
@@ -1,119 +0,0 @@
-> chr18_57379354_57380496 315 C T 0.014036
- BanI
- 1 CAGACTAGGCTTGGGGGTCTTGTCTCTGAACCAGAAGCCGTAAGCTGGGGTGGTGGAACT
- >>>>>>>>>>>>>>>>>>>>
-
- 61 CCATCCTCTGGAGGGGTAGAAGACAGAGCAGGGCACnACCACGCACAGGCCTTCTTGCAC
-
-
-121 CATCACAAACTCCTGCATCTGCAGC
- <<<<<<<<<<<<<<<<<<<<
-
-> chr18_48070585_48071386 514 C T 0.163186
-
- 1 ATTTCTCTTCTCAGGCCGGTTTAGTTGCACATGCAGAACATGTTTCTGGGCAGCTGTCAC
- >>>>>>>>>>>>>>>>>>>>
-
- 61 CCGAAGGGACTCATAGCTGTGGCCTGGGGCTTCCTCTGGGGATGCTTnGGAGGCTTCCTC
-
-
-121 TTGTGCAGAGGCACTCATTGGGCGAAGGCTGAGACCCAGGTTGGTGGAGGCTGTCAGTCC
- <<<<<
-
-181 TGGGGAGACAGAGGTAGG
- <<<<<<<<<<<<<<<
-
-> chr14_80021455_80022064 138 G A 0.194886
- Hsp92II
- 1 CGGGGCTGAAGGGATGGTTATGAAGGTGAGAAACAGGGGCCACCTGTCCCCAAGGTACCT
- >>>>>>>>>>>>>>>>>>>>
-
- 61 TGCGACnTGCCATCTGCGCTCCACCAGTAAATGGACGTCTTCGATCCTTCTGTTGTTGGC
- <<<<<<<<<<<<<
-
-121 GTAGTGCAAA
- <<<<<<<
-
-> chr19_39866997_39874915 3117 C T 0.946156
- BstOI
- 1 TTTCTCTTGAGTGGGAGTGACGGAAGGGCTGCTGTCCCCAGCCATGGGCACCCCnGGCAG
- >>>>>>>>>>>>>>>>>>>>
-
- 61 CGGGGGCAGGTCTGTGAGGGTGGGCTGCGTCTCCACCCTCAGCTGGTGCTCCAGCAGGGC
-
-
-121 TGTCTGCTGCCTGAGCTCCCGGTGCTTGCTCATTTCCTGCTCCAGCTCCTT
- <<<<<<<<<<<<<<<<<<<<
-
-> chr15_64470252_64471048 89 G A 1.325099
-
- 1 GTGTGTGTGTGTGTGCCTGTGTCTGTACATGCACACCACGTGGCCTCACCCAGTGCCCTC
- >>>>>>>>>>>>>>>>>>>>
-
- 61 AGCTCCATGGTGATGTCCACnTAGCCGTGCTCCGCGCTGTAGTACATGGCCTCCTGGAGG
-
-
-121 GCCTTGGTGCGCGTCCGGCTCAGGCGCATGGGCCCCTCGCTGCCGCTGCCCTGGCTGGAT
- <<<<<<
-
-181 GCATCGCTCTCTTCCAC
- <<<<<<<<<<<<<<
-
-> chr18_50154905_50155664 304 A G 0.578070
-
- 1 TGGTTTCTCTCTCCCCAGTACGCCCAGCAGTGGAACCAGTACTATCAGAACCAGGGCCAG
- >>>>>>>>>>>>>>>>>>>>
-
- 61 TGGCCGCCGTACTACGGGAACTATGACTnCGGGAGCTACTCCGGGAACACACAGGGGGGC
-
-
-121 ACAAGCGCACAGTAGCCACGTGCCCTGGAGGCCCCTGCCGGCTTCCTCCACCAGCGCCCG
-
-
-181 CCTCAGTCCTCCTCATCCATCCCTC
- <<<<<<<<<<<<<<<<<<<<
-
-> chr2_75111355_75112576 314 A C 0.613831
-
- 1 TTTGCCCTGAGGCAGACTTTTTAAAGTACTGTGTAATGTATGAAGTCCTTCTGCTCAAGC
- >>>>>>>>>>>>>>>>>>>>
-
- 61 AAATCATTGGCATGAAAACAGTTGCAAACTTATTGTGAGAGAAGAGTCCAAGAGTTTTAA
-
-
-121 CAGTCTGTAAGTATATAGCCTGTGAGTTTGATTTCCTTCTTGTTTTTnTTCCAGAAACAT
-
-
-181 GATCAGGGGCAAGTTCTATTGGATA
- <<<<<<<<<<<<<<<<<<<<
-
-> chr8_93901796_93905612 2471 A C 0.322555
- MboI,Sau3AI
- 1 GGGTTCATGGCAGAGTTGAGCACGGCCAGCACGATGAACCACTGGGCCTTGAACAGGATn
- >>>>>>>>>>>>>>>>>>>>
-
- 61 GCGCACTCCTTCACCTTGCAGGCCACATCCACAAGGAAAAGGATGAAGAGTGGGGACCAG
- <<<<<<<<<<<<<<<<<<<<
-
-121 C
-
-
-> chr10_7434473_7435447 524 T C 1.119264
-
- 1 CCTGGCAAAAGCAAAAGAGCAAAAATCTAGAAGnGGTAAGCATCTTCACTGTTTAGCACA
- >>>>>>>>>>>>>>>>>>>>
-
- 61 AATTAAATAGCACTTTGAATATGATGATTTCTGTGGTATTGTGTTATCTTACTTTTGAGA
-
-
-121 CAAATAATCGCTTTCAAATGAATATTTCTGAATGTTTGTCATCTCTGGCAAGGAAAT
- <<<<<<<<<<<<<<<<<<<<
-
-> chr19_14240610_14242055 232 C T 0.835026
-
- 1 TTTCTGTCATTGTTTGTGACGCAGAAGGGnTGCTGATGTGGAAAGCCTCAAGATGGAGAC
- >>>>>>>>>>>>>>>>>>>>
-
- 61 GGAAATGCTTTATCCCGAGATAACCGTAGAAGTGGGCAGAGTCACT
- <<<<<<<<<<<<<<<<<<<<
-
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.sample.wsf
--- a/test-data/gd.sample.wsf
+++ /dev/null
@@ -1,12 +0,0 @@
-#species=bighorn
-#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP
-chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
-chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
-chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
-chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
-chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
-chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0
-chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0
-chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
-chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
-chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_restriction_enzymes.wsf
--- a/test-data/gd.select_restriction_enzymes.wsf
+++ /dev/null
@@ -1,5 +0,0 @@
-#species=bighorn
-#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP
-chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
-chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
-chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 test-data/gd.select_snps.wsf
--- a/test-data/gd.select_snps.wsf
+++ /dev/null
@@ -1,7 +0,0 @@
-#species=bighorn
-#scaffold pos A B aa1 aa2 ref rPos rNuc rAA #desA #desB desQ #mtA #mtB mtQ pair sep Fst cons prim #RFLP
-chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
-chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
-chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
-chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
-chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.chrlens.loc.sample
--- a/tool-data/gd.chrlens.loc.sample
+++ /dev/null
@@ -1,22 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools to
-# use a directory of sequence length files. You will need to create these
-# sequence length files and then create a gd.chrlens.loc file similar to
-# this one (store it in this directory) that points to the directories
-# in which these sequence length files are stored. The gd.chrlens.loc
-# file has the following format (white space characters are TAB
-# characters):
-#
-#<species><reference_species_file_path>
-#
-# So, for example, if you used Monodelphis domestica as the reference
-# species for a collection of Sarcophilus harrisii SNPs, then the
-# gd.chrlens.loc entry would look like this:
-#
-#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
-#
-# Your gd.chrlens.loc file should include an entry for each pair of
-# species SNPs and reference species. For example:
-#
-#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt
-#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt
-#...etc...
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.primers.loc.sample
--- a/tool-data/gd.primers.loc.sample
+++ /dev/null
@@ -1,22 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools to
-# use a directory of primers files. You will need to create these primers
-# files and then create a gd.primers.loc file similar to this one (store
-# it in this directory) that points to the directories in which these
-# primers files are stored. The gd.primers.loc file has the following
-# format (white space characters are TAB characters):
-#
-#<species><primers_file_path>
-#
-# So, for example, if you had a primers file located at
-# /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of
-# Ovis canadensis SNPs, then the gd.primers.loc entry would look like
-# this:
-#
-#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
-#
-# Your gd.primers.loc file should include an entry for each pair of
-# species SNPs and primers file. For example:
-#
-#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt
-#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt
-#...etc...
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.restriction_enzymes.txt.sample
--- a/tool-data/gd.restriction_enzymes.txt.sample
+++ /dev/null
@@ -1,99 +0,0 @@
-Acc65I - GGTACC Acc65I
-AccB7I - CCANNNNNTGG AccB7I
-AccI - GT(A/C)(G/T)AC AccI
-AccIII - TCCGGA AccIII
-AcyI - G(A/G)CG(C/T)C AcyI
-AgeI - ACCGGT AgeI
-AluI - AGCT AluI
-Alw44I - GTGCAC Alw44I
-ApaI - GGGCCC ApaI
-AvaI - C(C/T)CG(A/G)G AvaI
-AvaII - GG(A/T)CC AvaII
-BalI - TGGCCA BalI
-BamHI - GGATCC BamHI
-BanI - GG(C/T)(A/G)CC BanI
-BanII - G(A/G)GC(C/T)C BanII
-BbuI - GCATGC BbuI
-BclI - TGATCA BclI
-BglI - GCCNNNNNGGC BglI
-BglII - AGATCT BglII
-BsaMI - GAATGC BsaMI
-BsaOI - CG(A/G)(C/T)CG BsaOI
-Bsp1286I - G(A/G/T)GC(A/C/T)C Bsp1286I
-BsrBRI - GATNNNNATC BsrBRI
-BsrSI - ACTGG BsrSI
-BssHII - GCGCGC BssHII
-Bst98I - CTTAAG Bst98I
-BstEII - GGTNACC BstEII
-BstOI - CC(A/T)GG BstOI
-BstXI - CCANNNNNNTGG BstXI
-BstZI - CGGCCG BstZI
-Bsu36I - CCTNAGG Bsu36I
-CfoI - GCGC CfoI
-ClaI - ATCGAT ClaI
-Csp45I - TTCGAA Csp45I
-CspI - CGG(A/T)CCG CspI
-DdeI - CTNAG DdeI
-DpnI - GATC DpnI
-DraI - TTTAAA DraI
-EclHKI - GACNNNNNGTC EclHKI
-Eco47III - AGCGCT Eco47III
-Eco52I - CGGCCG Eco52I
-Eco72I - CACGTG Eco72I
-EcoRI - GAATTC EcoRI
-EcoRV - GATATC EcoRV
-HaeII - (A/G)GCGC(C/T) HaeII
-HaeIII - GGCC HaeIII
-HhaI - GCGC HhaI
-HincII - GT(C/T)(A/G)AC HincII
-HindIII - AAGCTT HindIII
-HinfI - GANTC HinfI
-HpaI - GTTAAC HpaI
-HpaII - CCGG HpaII
-Hsp92I - G(A/G)CG(C/T)C Hsp92I
-Hsp92II - CATG Hsp92II
-I-PpoI - TAACTATGACTCTCTTAAGGTAGCCAAAT I-PpoI
-KpnI - GGTACC KpnI
-MboI - GATC MboI
-MluI - ACGCGT MluI
-MspA1I - C(A/C)GC(G/T)G MspA1I
-MspI - CCGG MspI
-NaeI - GCCGGC NaeI
-NarI - GGCGCC NarI
-NciI - CC(C/G)GG NciI
-NcoI - CCATGG NcoI
-NdeI - CATATG NdeI
-NgoMIV - GCCGGC NgoMIV
-NheI - GCTAGC NheI
-NotI - GCGGCCGC NotI
-NruI - TCGCGA NruI
-NsiI - ATGCAT NsiI
-PstI - CTGCAG PstI
-PvuI - CGATCG PvuI
-PvuII - CAGCTG PvuII
-RsaI - GTAC RsaI
-SacI - GAGCTC SacI
-SacII - CCGCGG SacII
-SalI - GTCGAC SalI
-Sau3AI - GATC Sau3AI
-Sau96I - GGNCC Sau96I
-ScaI - AGTACT ScaI
-SfiI - GGCCNNNNNGGCC SfiI
-SgfI - GCGATCGC SgfI
-SinI - GG(A/T)CC SinI
-SmaI - CCCGGG SmaI
-SnaBI - TACGTA SnaBI
-SpeI - ACTAGT SpeI
-SphI - GCATGC SphI
-SspI - AATATT SspI
-StuI - AGGCCT StuI
-StyI - CC(A/T)(A/T)GG StyI
-TaqI - TCGA TaqI
-Tru9I - TTAA Tru9I
-Tth111I - GACNNNGTC Tth111I
-VspI - ATTAAT VspI
-XbaI - TCTAGA XbaI
-XhoI - CTCGAG XhoI
-XhoII - (A/G)GATC(C/T) XhoII
-XmaI - CCCGGG XmaI
-XmnI - GAANNNNTTC XmnI
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.snps.loc.sample
--- a/tool-data/gd.snps.loc.sample
+++ /dev/null
@@ -1,21 +0,0 @@
-# This is a sample file distributed with Galaxy that enables tools to
-# use a directory of SNP call files. You will need to create these SNP
-# call files and then create a gd.snps.loc file similar to this one (store
-# it in this directory) that points to the directories in which these
-# SNP call files are stored. The gd.snps.loc file has the following
-# format (white space characters are TAB characters):
-#
-#<species><SNP_call_file_path>
-#
-# So, for example, if you had a SNP call file located at
-# /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of
-# Ovis canadensis SNPs, then the gd.snps.loc entry would look like this:
-#
-#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
-#
-# Your gd.snps.loc file should include an entry for each pair of species
-# SNPs and SNP call file. For example:
-#
-#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt
-#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt
-#...etc...
diff -r 0edea146c96436e63076550c595bcc444ba2cdb0 -r 0ffa2695e436501aa55546de6c4643743fe0d2f4 tool-data/gd.species.txt.sample
--- a/tool-data/gd.species.txt.sample
+++ /dev/null
@@ -1,3 +0,0 @@
-# genome diversity species
-tasmanian_devil Tasmanian devil
-bighorn bighorn
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0edea146c964/
changeset: 0edea146c964
user: jgoecks
date: 2012-04-09 22:17:46
summary: Comment out recently used tool update for now because it is not implemented yet.
affected #: 1 file
diff -r 507135da0b2c15ddbb05759c5d38a0ed0f429d0a -r 0edea146c96436e63076550c595bcc444ba2cdb0 templates/tool_executed.mako
--- a/templates/tool_executed.mako
+++ b/templates/tool_executed.mako
@@ -16,7 +16,7 @@
%if trans.user:
if (inside_galaxy_frameset)
{
- parent.frames.galaxy_tools.update_recently_used();
+ //parent.frames.galaxy_tools.update_recently_used();
}
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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