commit/galaxy-central: dan: Add argument names to parameter help for GATK tools' options.
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d59674927a52/ changeset: d59674927a52 user: dan date: 2012-04-10 22:22:45 summary: Add argument names to parameter help for GATK tools' options. affected #: 16 files diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/analyze_covariates.xml --- a/tools/gatk/analyze_covariates.xml +++ b/tools/gatk/analyze_covariates.xml @@ -24,7 +24,7 @@ ' </command><inputs> - <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" /> + <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file <recal_file>" /><conditional name="analysis_param_type"><param name="analysis_param_type_selector" type="select" label="Basic or Advanced options"><option value="basic" selected="True">Basic</option> @@ -34,11 +34,11 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number."/> - <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups."/> - <param name="max_quality_score" type="integer" value="50" label="Max quality score"/> - <param name="max_histogram_value" type="integer" value="0" label="Max histogram value"/> - <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality"/> + <param name="ignore_q" type="integer" value="5" label="Ignore bases with reported quality less than this number." help="-ignoreQ,--ignoreQ <ignoreQ> "/> + <param name="num_read_groups" type="integer" value="-1" label="Only process N read groups." help="-numRG,--numRG <numRG>"/> + <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score <max_quality_score>"/> + <param name="max_histogram_value" type="integer" value="0" label="Max histogram value" help="-maxHist,--max_histogram_value <max_histogram_value>"/> + <param name="do_indel_quality" type="boolean" truevalue="--do_indel_quality" falsevalue="" label="Do indel quality" help="--do_indel_quality"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -144,25 +144,28 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" > + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> - <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" /> - <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" > + <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" help="-standard,--standard_covs" /> + <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" help="-cov,--covariate <covariate>" ><!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --><option value="ReadGroupCovariate" /><option value="QualityScoreCovariate" /> @@ -178,7 +181,7 @@ <option value="TileCovariate" /></param> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-knownSites,--knownSites <knownSites>"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -427,7 +430,7 @@ </when><when value="advanced"><conditional name="default_read_group_type"> - <param name="default_read_group_type_selector" type="select" label="Set default Read Group"> + <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group"><option value="default" selected="True">Don't Set</option><option value="set">Set</option></param> @@ -438,14 +441,14 @@ <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/></when></conditional> - <param name="default_platform" type="select" label="Set default Platform"> + <param name="default_platform" type="select" label="Set default Platform" help="--default_platform"><option value="default" selected="True">Don't Set</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param><conditional name="force_read_group_type"> - <param name="force_read_group_type_selector" type="select" label="Force Read Group"> + <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group"><option value="default" selected="True">Don't Force</option><option value="set">Force</option></param> @@ -456,13 +459,13 @@ <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/></when></conditional> - <param name="force_platform" type="select" label="Force Platform"> + <param name="force_platform" type="select" label="Force Platform" help="--force_platform"><option value="default" selected="True">Don't Force</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param> - <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/> + <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/><conditional name="solid_options_type"><param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"><option value="default" selected="True">Don't Set</option> @@ -472,14 +475,14 @@ <!-- do nothing here --></when><when value="set"> - <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted"> + <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode <solid_recal_mode>"><option value="default" selected="True">Don't set</option><option value="DO_NOTHING">DO_NOTHING</option><option value="SET_Q_ZERO">SET_Q_ZERO</option><option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option><option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option></param> - <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls"> + <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy <solid_nocall_strategy>"><option value="default" selected="True">Don't set</option><option value="THROW_EXCEPTION">THROW_EXCEPTION</option><option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> @@ -487,8 +490,8 @@ </param></when></conditional> - <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/> - <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" /> + <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="window_size_nqs"/> + <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback <homopolymer_nback>" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -190,13 +190,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options> @@ -204,27 +204,26 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="input_bams" title="BAM file" min="1"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"> + <param name="input_bam" type="data" format="bam" label="BAM file" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" /> + <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes <calculateCoverageOverGenes>" /> - <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes"> + <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType <partitionType>"><option value="sample" selected="True">sample</option><option value="readgroup">readgroup</option><option value="library">library</option></param> - <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold"> + <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold <summaryCoverageThreshold>"><param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" /></repeat> - <param name="output_format" type="select" label="Output format" > + <param name="output_format" type="select" label="Output format" help="--outputFormat <outputFormat>" ><option value="csv">csv</option><option value="table">table</option><option value="rtable" selected="True">rtable</option> @@ -450,21 +449,21 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" /> - <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" /> - <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" /> - <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" /> - <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." /> - <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" /> - <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" /> - <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" /> - <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" /> - <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" /> - <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." /> - <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" /> - <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" /> - <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" /> - <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" /> + <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> + <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> + <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality <maxBaseQuality>" /> + <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality <minBaseQuality>" /> + <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality <maxMappingQuality>" /> + <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality <minMappingQuality>" /> + <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins <nBins>" /> + <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" /> + <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" /> + <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" /> + <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" /> + <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" /> + <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" /> + <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start <start>" /> + <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop <stop>" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -122,29 +122,28 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> - <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>"><options> - <filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> + <filter type="data_meta" key="dbkey" ref="input_bam" /></options></param></when></conditional> - <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"> + <param name="target_intervals" type="data" format="gatk_interval,bed,picard_interval_list" label="Restrict realignment to provided intervals" help="-targetIntervals,--targetIntervals <targetIntervals>" /> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--knownAlleles <knownAlleles>"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -167,8 +166,8 @@ </when></conditional></repeat> - <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" /> - <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs"/> + <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning <LODThresholdForCleaning>" /> + <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -391,19 +390,19 @@ </when><when value="advanced"> - <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" /> - <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/> - <param name="consensus_determination_model" type="select" label="Consensus Determination Model"> + <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold <entropyThreshold>" /> + <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> + <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel <consensusDeterminationModel>"><option value="KNOWNS_ONLY">KNOWNS_ONLY</option><option value="USE_READS" selected="True">USE_READS</option><option value="USE_SW">USE_SW</option></param> - <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" /> - <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" /> - <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" /> - <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" /> - <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" /> - <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam"/> + <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement <maxIsizeForMovement>" /> + <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed <maxPositionalMoveAllowed>" /> + <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses <maxConsensuses>" /> + <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses <maxReadsForConsensuses>" /> + <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment <maxReadsForRealignment>" /> + <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/print_reads.xml --- a/tools/gatk/print_reads.xml +++ b/tools/gatk/print_reads.xml @@ -106,13 +106,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options> @@ -120,21 +120,21 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"><param name="input_bam" type="data" format="bam" label="BAM file" ></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" /> - <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" /> - <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" /> - <repeat name="sample_file_repeat" title="File containing a list of samples to include"> + <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" help="-n,--number <number>" /> + <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform <platform>" /> + <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup <readGroup>" /> + <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file <sample_file>"><param name="input_sample_file" type="data" format="text" label="Sample file" /></repeat> - <repeat name="sample_name_repeat" title="Sample name to be included in the analysis"> + <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name <sample_name>"><param name="sample_name" type="text" label="Sample name" /></repeat> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -110,11 +110,11 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> @@ -122,17 +122,16 @@ </param></when><when value="history"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> - <param name="ref_file" type="data" format="fasta" label="Using reference file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>"><options> - <filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! --> + <filter type="data_meta" key="dbkey" ref="input_bam" /></options></param></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known <known>"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -376,10 +375,10 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" /> - <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1"/> - <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" /> - <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" /> + <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize <windowSize>" /> + <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction <mismatchFraction>)"/> + <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus <minReadsAtLocus>" /> + <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize <maxIntervalSize>" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -120,28 +120,31 @@ #end if </command><inputs> - <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" /> + <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file <recal_file>" /><conditional name="reference_source"><param name="reference_source_selector" type="select" label="Choose the source for the reference list"><option value="cached">Locally cached</option><option value="history">History</option></param><when value="cached"> - <param name="input_bam" type="data" format="bam" label="BAM file"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>" ><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options><validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when> - <when value="history"><!-- FIX ME!!!! --> - <param name="input_bam" type="data" format="bam" label="BAM file" > + <when value="history"> + <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file <input_file>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>"> + <options> + <filter type="data_meta" key="dbkey" ref="input_bam" /> + </options></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional> @@ -367,7 +370,7 @@ </when><when value="advanced"><conditional name="default_read_group_type"> - <param name="default_read_group_type_selector" type="select" label="Set default Read Group"> + <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group"><option value="default" selected="True">Don't Set</option><option value="set">Set</option></param> @@ -378,14 +381,14 @@ <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/></when></conditional> - <param name="default_platform" type="select" label="Set default Platform"> + <param name="default_platform" type="select" label="Set default Platform" help="--default_platform"><option value="default" selected="True">Don't Set</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param><conditional name="force_read_group_type"> - <param name="force_read_group_type_selector" type="select" label="Force Read Group"> + <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group"><option value="default" selected="True">Don't Force</option><option value="set">Force</option></param> @@ -396,13 +399,13 @@ <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/></when></conditional> - <param name="force_platform" type="select" label="Force Platform"> + <param name="force_platform" type="select" label="Force Platform" help="--force_platform"><option value="default" selected="True">Don't Force</option><option value="illumina">illumina</option><option value="454">454</option><option value="solid">solid</option></param> - <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/> + <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/><conditional name="solid_options_type"><param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"><option value="default" selected="True">Don't Set</option> @@ -412,14 +415,14 @@ <!-- do nothing here --></when><when value="set"> - <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted"> + <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode <solid_recal_mode>"><option value="default" selected="True">Don't set</option><option value="DO_NOTHING">DO_NOTHING</option><option value="SET_Q_ZERO">SET_Q_ZERO</option><option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option><option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option></param> - <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls"> + <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy <solid_nocall_strategy>"><option value="default" selected="True">Don't set</option><option value="THROW_EXCEPTION">THROW_EXCEPTION</option><option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> @@ -427,13 +430,13 @@ </param></when></conditional> - <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/> - <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/> - <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" /> - <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated"/> - <param name="smoothing" type="integer" value="1" label="smoothing"/> - <param name="max_quality_score" type="integer" value="50" label="Max quality score"/> - <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag"/> + <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> + <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/> + <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback <homopolymer_nback>" /> + <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than <preserve_qscores_less_than>"/> + <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing <smoothing>"/> + <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score <max_quality_score>"/> + <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -155,13 +155,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--></options> @@ -169,15 +169,15 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="input_bams" title="Sample BAM file" min="1"> + <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file <input_file>"><param name="input_bam" type="data" format="bam" label="BAM file" ></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-D,--dbsnp <dbsnp>"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -201,14 +201,14 @@ </conditional></repeat> - <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ"> + <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model <genotype_likelihoods_model>"><option value="BOTH" selected="True">BOTH</option><option value="SNP">SNP</option><option value="INDEL">INDEL</option></param> - <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" /> - <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" /> + <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling <standard_min_confidence_threshold_for_calling>" /> + <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting <standard_min_confidence_threshold_for_emitting>" /><conditional name="gatk_param_type"> @@ -431,14 +431,14 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ"> + <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model <p_nonref_model>"><option value="EXACT" selected="True">EXACT</option><option value="GRID_SEARCH">GRID_SEARCH</option></param> - <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" /> - <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" /> + <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity <heterozygosity>" /> + <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate <pcr_error_rate>" /><conditional name="genotyping_mode_type"> - <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping"> + <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode <genotyping_mode>"><option value="DISCOVERY" selected="True">DISCOVERY</option><option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option></param> @@ -446,32 +446,32 @@ <!-- Do nothing here --></when><when value="GENOTYPE_GIVEN_ALLELES"> - <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" /> + <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles <alleles>" /></when></conditional> - <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?"> + <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode <output_mode>"><option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option><option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option><option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option></param> - <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" /> - <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" /> - <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1" /> - <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" /> - <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" /> - <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125"/> - <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" /> - <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="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" /> + <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score <min_base_quality_score>" /> + <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction <max_deletion_fraction>)" /> + <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles <max_alternate_alleles>" /> + <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping <min_indel_count_for_genotyping>" /> + <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity <indel_heterozygosity>)"/> + <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" /> + <param name="indelGapOpenPenalty" type="float" value="45.0" label="Indel gap open penalty" help="--indelGapOpenPenalty" /> + <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> + <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> + <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation <annotation>"><!-- 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> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation <annotation>"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat><!-- @@ -488,7 +488,7 @@ </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" help="-G,--group <group>"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option> @@ -497,14 +497,14 @@ <!-- <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" > + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation <excludeAnnotation>" ><!-- 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 name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" /> + <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" /></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -150,13 +150,13 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." > + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant <variant>"/> + <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file <input_file>)" ><validator type="unspecified_build" /><validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -164,11 +164,11 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /> - <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" > + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant <variant>"/> + <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/> + <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file <input_file>)" ></param> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional><conditional name="annotations_type"> @@ -180,7 +180,7 @@ <!-- no extra options here --></when><when value="choose"> - <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > + <param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" help="-A,--annotation <annotation>" ><!-- 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=","/> @@ -190,17 +190,17 @@ </when></conditional> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation <annotation>"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> - <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp <comp>"><param name="comp_input_rod" type="data" format="vcf" label="ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="ROD Name"/></repeat><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp <dbsnp>"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -213,13 +213,13 @@ </when></conditional> - <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data"> + <repeat name="resource_rod_bind" title="Binding for reference-ordered resource data" help="-resource,--resource <resource>"><param name="resource_input_rod" type="data" format="vcf" label="ROD file" /><param name="resource_rod_name" type="text" value="Unnamed" label="ROD Name"/></repeat><conditional name="snpEff_rod_bind_type"> - <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> + <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile <snpEffFile>"><option value="set_snpEff">Set snpEff</option><option value="exclude_snpEff" selected="True">Don't set snpEff</option></param> @@ -232,7 +232,7 @@ </when></conditional> - <repeat name="expressions" title="Expression"> + <repeat name="expressions" title="Expression" help="-E,--expression <expression>"><param name="expression" type="text" value="" label="Expression"/></repeat> @@ -447,16 +447,16 @@ </when></conditional> - <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls"> + <param name="annotation_group" type="select" multiple="True" display="checkboxes" label="annotation interfaces/groups to apply to variant calls" help="-G,--group <group>"><option value="RodRequiringAnnotation">RodRequiringAnnotation</option><option value="Standard">Standard</option><option value="Experimental">Experimental</option><option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option></param> - <param name="family_string" type="text" value="" label="Family String"/> - <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/> - <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > + <param name="family_string" type="text" value="" label="Family String" help="--family_string"/> + <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio." help="-mvq,--MendelViolationGenotypeQualityThreshold <MendelViolationGenotypeQualityThreshold>"/> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation <excludeAnnotation>" ><!-- 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=","/> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -104,12 +104,12 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> - <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> + <repeat name="variants" title="Variant" min="1" help="-input,--input <input>"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/></repeat> - <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /> - <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file <recal_file>" /> + <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file <tranches_file>" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options> @@ -117,12 +117,12 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input <input>"><param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /></repeat> - <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /> - <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file <recal_file>" /> + <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file <tranches_file>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> @@ -337,12 +337,12 @@ </when></conditional> - <param name="mode" type="select" label="Recalibration mode"> + <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode <mode>"><option value="SNP" selected="True">SNP</option><option value="INDEL">INDEL</option><option value="BOTH">BOTH</option></param> - <repeat name="ignore_filters" title="Ignore Filter"> + <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter <ignore_filter>"><conditional name="ignore_filter_type"><param name="ignore_filter_type_selector" type="select" label="Filter Type"><option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> @@ -352,9 +352,11 @@ <when value="custom"><param name="filter_name" type="text" value="" label="Filter name"/></when> + <when value="HARD_TO_VALIDATE" /> + <when value="LowQual" /></conditional></repeat> - <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/> + <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level <ts_filter_level>"/></inputs><outputs><data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" /> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -115,13 +115,13 @@ <option value="history">History</option></param><when value="cached"> - <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant <variant>)"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /></param></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variants.input_variant" column="dbkey"/> --></options> @@ -129,17 +129,17 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here."> + <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant <variant>)"><param name="input_variant" type="data" format="vcf" label="Input variant file" /><param name="input_variant_name" type="text" value="" label="Variant name" help="Names must be unique"><validator type="length" min="1" message="You must provide a unique name for this set of variants" /></param></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" > + <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption <genotypemergeoption>" ><option value="UNIQUIFY" /><option value="PRIORITIZE" selected="true"/><option value="UNSORTED" /> @@ -367,18 +367,18 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields? " > + <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype <filteredrecordsmergetype>" ><option value="KEEP_IF_ANY_UNFILTERED" selected="true"/><option value="KEEP_IF_ALL_UNFILTERED" /></param> - <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" /> - <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" /> - <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" /> + <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" /> + <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" /> + <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" /> - <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from."/> - <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." /> - <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files."/> + <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey <setKey>"/> + <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" /> + <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN <minimumN>"/></when></conditional> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -163,10 +163,10 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval <eval>"><param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --></options> @@ -174,21 +174,21 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-eval,--eval <eval>"><param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data"> + <repeat name="comp_rod_bind" title="Binding for reference-ordered comparison data" help="-comp,--comp <comp>"><param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /><param name="comp_rod_name" type="text" value="Unnamed" label="Comparison ROD Name"/> - <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" /> + <param name="comp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use Comparison ROD as known_names" help="-knownName,--known_names <known_names>"/></repeat><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp <dbsnp>"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -198,7 +198,7 @@ <when value="set_dbsnp"><param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" /><param name="dbsnp_rod_name" type="hidden" value="dbsnp" label="dbSNP ROD Name"/> - <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" /> + <param name="dbsnp_known_names" type="boolean" truevalue="--known_names" falsevalue="" label="Use dbSNP ROD as known_names" help="-knownName,--known_names <known_names>" /></when></conditional> @@ -424,7 +424,7 @@ </when><when value="advanced"><repeat name="stratifications" title="Stratification"> - <param name="select_exps" value="" type="text" label="Stratification Expression"> + <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps <select_exps>"><sanitizer><valid initial="string.printable"><remove value="'"/> @@ -432,14 +432,14 @@ <mapping initial="none"/></sanitizer></param> - <param name="select_name" value="" type="text" label="Name"/> + <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names <select_names>"/></repeat> - <repeat name="samples" title="Sample"> + <repeat name="samples" title="Sample" help="-sn,--sample <sample>"><param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/></repeat> - <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" > + <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule <stratificationModule>" ><!-- do these need individual options also? gatk wiki has little info --><option value="AlleleFrequency" /><option value="AlleleCount" /> @@ -454,13 +454,13 @@ <option value="Sample" /><option value="IntervalStratification" /></param> - <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" /> + <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" /> - <repeat name="only_variants_of_type" title="only Variants Of Type"> + <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"><param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/></repeat> - <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" > + <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule <evalModule>" ><!-- do these need individual options also? gatk wiki has little info --><option value="ACTransitionTable" /><option value="AlleleFrequencyComparison" /> @@ -479,15 +479,15 @@ <option value="TiTvVariantEvaluator" /><option value="VariantQualityScore" /></param> - <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" /> + <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" /> - <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file " value="0"/> - <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0"/> - <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined"/> - <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50"/> - <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" /> - <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" /> - <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" /> + <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples <numSamples>"/> + <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality <minPhaseQuality>"/> + <param name="family" type="text" value="" label="If provided, genotypes in will be examined for mendelian violations: this argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined" help="--family_structure"/> + <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold <mendelianViolationQualThreshold>"/> + <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments <ancestralAlignments>" /> + <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs <knownCNVs>" /> + <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals <stratIntervals>" /></when></conditional> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -109,8 +109,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant <variant>" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -118,14 +118,14 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant <variant>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional><repeat name="variant_filters" title="Variant Filters"> - <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions"> + <param name="filter_expression" value="AB < 0.2 || MQ0 > 50" type="text" label="Filter expression" help="JEXL formatted expressions (-filter,--filterExpression <filterExpression>)"><sanitizer><valid initial="string.printable"><remove value="'"/> @@ -133,8 +133,8 @@ <mapping initial="none"/></sanitizer></param> - <param name="filter_name" value="custom_filter" type="text" label="Filter name"/> - <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" /> + <param name="filter_name" value="custom_filter" type="text" label="Filter name" help="-filterName,--filterName <filterName>"/> + <param name="is_genotype_filter" type="boolean" truevalue="genotypeFilter" falsevalue="filter" label="Use filter at the individual sample level" help="Use -G_filter,--genotypeFilterExpression <genotypeFilterExpression> and -G_filterName,--genotypeFilterName <genotypeFilterName> for filter type" /></repeat> @@ -148,9 +148,9 @@ <!-- Do nothing here --></when><when value="set_mask"> - <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" /> - <param name="mask_rod_name" type="text" value="Mask" label="Mask Name"/> - <param name="mask_extension" type="integer" value="0" label="Mask Extension"/> + <param name="input_mask_rod" type="data" format="bed,gatk_dbsnp,vcf" label="Mask ROD file" help="--mask <mask>" /> + <param name="mask_rod_name" type="text" value="Mask" label="Mask Name" help="-maskName,--maskName <maskName>"/> + <param name="mask_extension" type="integer" value="0" label="Mask Extension" help="-maskExtend,--maskExtension <maskExtension>"/></when></conditional> @@ -375,12 +375,12 @@ <!-- Do nothing here --></when><when value="cluster_snp"> - <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster "/> - <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs"/> + <param name="cluster_size" type="integer" value="3" label="The number of SNPs which make up a cluster" help="-cluster,--clusterSize <clusterSize>"/> + <param name="cluster_window_size" type="integer" value="0" label="The window size (in bases) in which to evaluate clustered SNPs" help="-window,--clusterWindowSize <clusterWindowSize>"/></when></conditional> - <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" /> + <param name="missing_values_in_expressions_should_evaluate_as_failing" type="boolean" truevalue="--missingValuesInExpressionsShouldEvaluateAsFailing" falsevalue="" label="Should missing values be considered failing the expression" help="--missingValuesInExpressionsShouldEvaluateAsFailing" /></inputs><outputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -34,9 +34,9 @@ #end if #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": - -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #else: - -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" + -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" #end if #end for @@ -156,10 +156,10 @@ <option value="history">History</option></param><when value="cached"> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input <input>"><param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --></options> @@ -167,14 +167,14 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1"> + <repeat name="variants" title="Variant" min="1" help="-input,--input <input>"><param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <repeat name="rod_bind" title="Binding for reference-ordered data"> + <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource <resource>"><conditional name="rod_bind_type"><param name="rod_bind_type_selector" type="select" label="Binding Type"><option value="dbsnp" selected="True">dbSNP</option> @@ -185,6 +185,7 @@ <option value="omni">OMNI</option><option value="mask">Mask</option><option value="custom">Custom</option> + <option value="comp">Comp</option></param><when value="variant"><param name="input_rod" type="data" format="vcf" label="Variant ROD file" /> @@ -225,6 +226,25 @@ </when></conditional></when> + <when value="mask"> + <param name="input_rod" type="data" format="vcf" label="ROD file" /> + <conditional name="rod_training_type"> + <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> + <option value="is_training_truth_known">Set training/truth/known sites</option> + <option value="not_training_truth_known" selected="True">Don't Set options</option> + </param> + <when value="not_training_truth_known"> + <!-- do nothing here --> + </when> + <when value="is_training_truth_known"> + <param name="known" type="boolean" label="Is Known Site" truevalue="true" falsevalue="false"/> + <param name="training" type="boolean" label="Is Training Site" truevalue="true" falsevalue="false"/> + <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> + <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> + <param name="prior" type="float" label="prior probability of being true" value="12.0"/> + </when> + </conditional> + </when><when value="dbsnp"><param name="input_rod" type="data" format="vcf" label="ROD file" /><conditional name="rod_training_type"> @@ -343,7 +363,7 @@ </conditional></repeat> - <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations"> + <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation <use_annotation>"><!-- 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=","/> @@ -351,11 +371,11 @@ </options></param> - <repeat name="additional_annotations" title="Additional annotation"> + <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation <use_annotation>"><param name="additional_annotation_name" type="text" value="" label="Annotation name" /></repeat> - <param name="mode" type="select" label="Recalibration mode"> + <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode <mode>"><option value="SNP" selected="True">SNP</option><option value="INDEL">INDEL</option><option value="BOTH">BOTH</option> @@ -581,29 +601,29 @@ <!-- Do nothing here --></when><when value="advanced"> - <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10"/> - <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100"/> - <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30"/> - <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0"/> - <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0"/> - <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0"/> - <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001"/> - <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0"/> + <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="10" help="-mG,--maxGaussians <maxGaussians>"/> + <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="100" help="-mI,--maxIterations <maxIterations>"/> + <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="30" help="-nKM,--numKMeans <numKMeans>"/> + <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="8.0" help="-std,--stdThreshold <stdThreshold>"/> + <param name="qual_threshold" type="float" label="If a known variant has raw QUAL value less than -qual then don't use it for building the Gaussian mixture model." value="80.0" help="-qual,--qualThreshold <qualThreshold>"/> + <param name="shrinkage" type="float" label="shrinkage parameter in variational Bayes algorithm" value="1.0" help="-shrinkage,--shrinkage <shrinkage>"/> + <param name="dirichlet" type="float" label="dirichlet parameter in variational Bayes algorithm" value="0.001" help="-dirichlet,--dirichlet <dirichlet>"/> + <param name="prior_counts" type="float" label="number of prior counts to use in variational Bayes algorithm" value="20.0" help="-priorCounts,--priorCounts <priorCounts>"/><conditional name="bad_variant_selector"><param name="bad_variant_selector_type" type="select" label="How to specify bad variants"><option value="percent" selected="True">Percent</option><option value="min_num">Number</option></param><when value="percent"> - <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03"/> + <param name="percent_bad_variants" type="float" label="percentage of the worst scoring variants to use when building the Gaussian mixture model of bad variants. 0.07 means bottom 7 percent." value="0.03" help="-percentBad,--percentBadVariants <percentBadVariants>"/></when><when value="min_num"> - <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000"/> + <param name="min_num_bad_variants" type="integer" label="minimum amount of worst scoring variants to use when building the Gaussian mixture model of bad variants. Will override -percentBad arugment if necessary" value="2000" help="-minNumBad,--minNumBadVariants <minNumBadVariants>"/></when></conditional> - <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15"/> - <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0"/> - <repeat name="ignore_filters" title="Ignore Filter"> + <param name="target_titv" type="float" label="expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (approx 2.15 for whole genome experiments). ONLY USED FOR PLOTTING PURPOSES!" value="2.15" help="-titv,--target_titv <target_titv>"/> + <param name="ts_tranche" type="text" label="levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)" value="100.0, 99.9, 99.0, 90.0" help="-tranche,--TStranche <TStranche>"/> + <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter <ignore_filter>"><conditional name="ignore_filter_type"><param name="ignore_filter_type_selector" type="select" label="Filter Type"><option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> @@ -613,9 +633,11 @@ <when value="custom"><param name="filter_name" type="text" value="" label="Filter name"/></when> + <when value="HARD_TO_VALIDATE" /> + <when value="LowQual" /></conditional></repeat> - <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0"/> + <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level <ts_filter_level>"/></when></conditional></inputs> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variant_select.xml --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -162,8 +162,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant <variant>" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -171,12 +171,12 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_variant" type="data" format="vcf" label="Variant file to select" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant <variant>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional> - <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data"> + <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions <select_expressions>"><param name="select_expressions" type="text" label="JEXL expression"><sanitizer><valid initial="string.printable"> @@ -187,18 +187,18 @@ </param></repeat> - <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True"/> - <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True"/> + <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance <concordance>"/> + <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance <discordance>"/> - <repeat name="sample_name_repeat" title="Include Samples by name"> + <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name <sample_name>"><param name="sample_name" type="text" label="Include genotypes from this sample"/></repeat> - <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name"> + <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name <exclude_sample_name>"><param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/></repeat> - <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" /> + <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" /><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> @@ -422,31 +422,31 @@ </when><when value="advanced"> - <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file"> + <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file <exclude_sample_file>"><param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/></repeat> - <repeat name="sample_file_repeat" title="Samples by file"> + <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file <sample_file>"><param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /></repeat> - <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True"/> + <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs <keepIDs>"/> - <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" /> + <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" /> - <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" /> + <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" /> - <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" /> + <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold <mendelianViolationQualThreshold>" /> - <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" /> + <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes <remove_fraction_genotypes>" /> - <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity"> + <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo <restrictAllelesTo>"><option value="ALL" selected="True">ALL</option><option value="MULTIALLELIC">MULTIALLELIC</option><option value="BIALLELIC">BIALLELIC</option></param> - <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided"> + <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions <sample_expressions>"><param name="sample_expressions" type="text" label="Regular expression"><sanitizer><valid initial="string.printable"> @@ -467,16 +467,16 @@ <!-- Do nothing here --></when><when value="select_random_fraction"> - <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1"/> + <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction <select_random_fraction>"/></when><when value="select_random_number"> - <param name="select_random_number" type="integer" value="0" label="Count" /> + <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number <select_random_number>" /></when></conditional> - <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" /> + <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" /> - <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes"> + <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude <selectTypeToInclude>"><option value="INDEL">INDEL</option><option value="SNP">SNP</option><option value="MIXED">MIXED</option> diff -r 25edd75ca72fd9c276476203e05c093e949b37eb -r d59674927a521dec8619441ac8801807e150392d tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -95,8 +95,8 @@ <option value="history">History</option></param><when value="cached"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - <param name="ref_file" type="select" label="Using reference genome"> + <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant <variant>" /> + <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence <reference_sequence>"><options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> @@ -104,13 +104,13 @@ </param></when><when value="history"><!-- FIX ME!!!! --> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant <variant>" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence <reference_sequence>" /></when></conditional><conditional name="dbsnp_rod_bind_type"> - <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file"> + <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP reference-ordered data file" help="-D,--dbsnp <dbsnp>"><option value="set_dbsnp" selected="True">Set dbSNP</option><option value="exclude_dbsnp">Don't set dbSNP</option></param> @@ -123,8 +123,8 @@ </when></conditional> - <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen. "/> - <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed. "/> + <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/> + <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/><conditional name="gatk_param_type"><param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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