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