Mercurial > repos > iuc > gatk2
changeset 13:669a23f1f4b5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
| author | iuc |
|---|---|
| date | Tue, 13 Oct 2015 17:22:38 -0400 |
| parents | 86007c982f00 |
| children | dbd9d574e68a |
| files | depth_of_coverage.xml gatk2_macros.xml haplotype_caller.xml unified_genotyper.xml variant_apply_recalibration.xml variant_eval.xml variant_recalibrator.xml variant_select.xml |
| diffstat | 8 files changed, 71 insertions(+), 109 deletions(-) [+] |
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--- a/depth_of_coverage.xml Thu May 14 22:47:18 2015 -0400 +++ b/depth_of_coverage.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0"> +<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1"> <description>on BAM files</description> <macros> <import>gatk2_macros.xml</import> @@ -8,12 +8,7 @@ <command interpreter="python">gatk2_wrapper.py ##--max_jvm_heap_fraction "1" --stdout "${output_log}" - #for $i, $input_bam in enumerate( $reference_source.input_bams ): - -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" - #if str( $input_bam.input_bam.metadata.bam_index ) != "None": - -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index - #end if - #end for + @BAM_INPUTS@ -p ' @JAR_PATH@ -T "DepthOfCoverage" @@ -129,12 +124,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> - </param> - </repeat> + <expand macro="input_bams_cached" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> @@ -143,9 +133,8 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> - </repeat> + + <expand macro="input_bams_history" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>
--- a/gatk2_macros.xml Thu May 14 22:47:18 2015 -0400 +++ b/gatk2_macros.xml Tue Oct 13 17:22:38 2015 -0400 @@ -24,11 +24,31 @@ -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" #end if </token> + <token name="@BAM_INPUTS@"> + #for $i, $input_bam in enumerate( $reference_source.input_bams ): + -d "-I" "${input_bam}" "${input_bam.ext}" "gatk_input_${i}" + #if str( $input_bam.metadata.bam_index ) != "None": + -d "" "${input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index + #end if + #end for + </token> + <xml name="input_variants" token_help="-input,--input &lt;input&gt;"> + <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" min="1" help="@HELP@"/> + </xml> + <xml name="input_bams_history"> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="True" min="1" help="-I,--input_file &lt;input_file&gt;"/> + </xml> + <xml name="input_bams_cached"> + <param name="input_bams" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" min="1" multiple="True"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_data_table" table_name="gatk2_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> + </xml> <template name="standard_gatk_options"> ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": - #for $pedigree in $gatk_param_type.pedigree: - -p '--pedigree "${pedigree.pedigree_file}"' + #for $pedigree in $gatk_param_type.pedigree_files: + -p '--pedigree "${pedigree}"' #end for #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: -p '--pedigreeString "${pedigree_string.pedigree_string}"' @@ -51,12 +71,12 @@ #end for ' #end for - #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): - -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_intervals ): + -d "--intervals" "${input_interval}" "${input_interval.ext}" "input_intervals_${interval_count}" #end for - - #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): - -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + + #for $interval_count, $input_interval in enumerate( $gatk_param_type.input_exclude_intervals ): + -d "--excludeIntervals" "${input_interval}" "${input_interval.ext}" "input_exlude_intervals_${interval_count}" #end for -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"' @@ -84,7 +104,7 @@ #end if #end for #end if - + #if str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -100,9 +120,7 @@ <!-- Do nothing here --> </when> <when value="advanced"> - <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &lt;pedigree&gt;"> - <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/> - </repeat> + <param name="pedigree_files" type="data" format="txt" label="Pedigree files for samples" multiple="True" help="-ped,--pedigree &lt;pedigree&gt;"/> <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &lt;pedigreeString&gt;"> <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/> </repeat> @@ -212,13 +230,9 @@ </when> </conditional> </repeat> - <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;"> - <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> - </repeat> - <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;"> - <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" /> - </repeat> - + <param name="input_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Operate on Genomic intervals" help="-L,--intervals &lt;intervals&gt;" /> + <param name="input_exclude_intervals" multiple="True" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Exclude Genomic intervals" help="-XL,--excludeIntervals &lt;excludeIntervals&gt;" /> + <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &lt;interval_set_rule&gt;"> <option value="UNION" selected="True">UNION</option> <option value="INTERSECTION">INTERSECTION</option> @@ -282,7 +296,7 @@ <option value="ALL" selected="True">ALL</option> <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option> </param> - + <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &lt;read_group_black_list&gt;"> <conditional name="read_group_black_list_type"> <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> @@ -297,7 +311,7 @@ </when> </conditional> </repeat> - + <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/> <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/> <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/> @@ -327,7 +341,7 @@ </xml> <xml name="allow_n_cigar_reads"> - <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue="" + <param name="allow_n_cigar_reads" type="boolean" truevalue="-U ALLOW_N_CIGAR_READS" falsevalue="" label="Allow N in CIGAR strings" help="This is required for RNA-seq data. (-U ALLOW_N_CIGAR_READS)" /> </xml>
--- a/haplotype_caller.xml Thu May 14 22:47:18 2015 -0400 +++ b/haplotype_caller.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.1"> +<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.2"> <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description> <macros> <import>gatk2_macros.xml</import> @@ -8,12 +8,7 @@ <command interpreter="python"> gatk2_wrapper.py --stdout "${output_log}" - #for $i, $input_bam in enumerate( $reference_source.input_bams ): - -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" - #if str( $input_bam.input_bam.metadata.bam_index ) != "None": - -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index - #end if - #end for + @INPUT_BAMS@ -p ' @JAR_PATH@ -T "HaplotypeCaller" @@ -119,12 +114,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> - </param> - </repeat> + <expand macro="input_bams_cached" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" > <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> @@ -133,9 +123,7 @@ </param> </when> <when value="history"> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file" /> - </repeat> + <expand macro="input_bams_history" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>
--- a/unified_genotyper.xml Thu May 14 22:47:18 2015 -0400 +++ b/unified_genotyper.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.1"> +<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.2"> <description>SNP and indel caller</description> <macros> <import>gatk2_macros.xml</import> @@ -8,12 +8,7 @@ <command interpreter="python"> gatk2_wrapper.py --stdout "${output_log}" - #for $i, $input_bam in enumerate( $reference_source.input_bams ): - -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" - #if str( $input_bam.input_bam.metadata.bam_index ) != "None": - -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index - #end if - #end for + @BAM_INPUTS@ -p ' @JAR_PATH@ -T "UnifiedGenotyper" @@ -89,12 +84,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_data_table" table_name="gatk2_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> + <expand macro="input_bams_cached" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> @@ -103,10 +93,7 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> - <param name="input_bam" type="data" format="bam" label="BAM file" > - </param> - </repeat> + <expand macro="input_bams_history" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>
--- a/variant_apply_recalibration.xml Thu May 14 22:47:18 2015 -0400 +++ b/variant_apply_recalibration.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0"> +<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.1"> <description></description> <macros> <import>gatk2_macros.xml</import> @@ -8,8 +8,8 @@ <command interpreter="python"> gatk2_wrapper.py --stdout "${output_log}" - #for $var_count, $variant in enumerate( $reference_source.variants ): - -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" + #for $var_count, $variant in enumerate( $reference_source.input_variants ): + -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" #end for -p ' @JAR_PATH@ @@ -46,9 +46,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/> - </repeat> + <expand macro="input_variants" /> <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> @@ -59,9 +57,7 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> - </repeat> + <expand macro="input_variants" /> <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
--- a/variant_eval.xml Thu May 14 22:47:18 2015 -0400 +++ b/variant_eval.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0"> +<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1"> <description></description> <macros> <import>gatk2_macros.xml</import> @@ -10,8 +10,8 @@ gatk2_wrapper.py --stdout "${output_log}" - #for $var_count, $variant in enumerate( $reference_source.variants ): - -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" + #for $var_count, $variant in enumerate( $reference_source.input_variants ): + -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" #end for -p ' @JAR_PATH@ @@ -100,9 +100,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - </repeat> + <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;"/> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> @@ -111,9 +109,7 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1" help="-eval,--eval &lt;eval&gt;"> - <param name="input_variant" type="data" format="vcf" label="Input variant file" /> - </repeat> + <expand macro="input_variants" help="-eval,--eval &lt;eval&gt;" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>
--- a/variant_recalibrator.xml Thu May 14 22:47:18 2015 -0400 +++ b/variant_recalibrator.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0"> +<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1"> <description></description> <macros> <import>gatk2_macros.xml</import> @@ -10,8 +10,8 @@ <command interpreter="python"> gatk2_wrapper.py --stdout "${output_log}" - #for $var_count, $variant in enumerate( $reference_source.variants ): - -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" + #for $var_count, $variant in enumerate( $reference_source.input_variants ): + -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}" #end for -p ' @JAR_PATH@ @@ -94,9 +94,7 @@ <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> - </repeat> + <expand macro="input_variants" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> @@ -105,9 +103,7 @@ </param> </when> <when value="history"> <!-- FIX ME!!!! --> - <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> - <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /> - </repeat> + <expand macro="input_variants" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional>
--- a/variant_select.xml Thu May 14 22:47:18 2015 -0400 +++ b/variant_select.xml Tue Oct 13 17:22:38 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.0"> +<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2"> <description>from VCF files</description> <macros> <import>gatk2_macros.xml</import> @@ -50,12 +50,12 @@ ##start tool specific options #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced': -p ' - #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat: - --exclude_sample_file "${exclude_sample_file.exclude_sample_file}" + #for $esf in $analysis_param_type.exclude_sample_file: + --exclude_sample_file "${esf}" #end for - #for $sample_file in $analysis_param_type.sample_file_repeat: - --sample_file "${ample_file.sample_file}" + #for $sf in $analysis_param_type.sample_file: + --sample_file "${sf}" #end for #if $analysis_param_type.input_keep_ids: @@ -143,15 +143,11 @@ <expand macro="analysis_type_conditional"> - <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;"> - <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/> - </repeat> + <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &lt;exclude_sample_file&gt;)"/> - <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &lt;sample_file&gt;"> - <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" /> - </repeat> + <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file" help="File containing a list of samples (one per line) to include (-sf,--sample_file &lt;sample_file&gt;)"/> - <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 &lt;keepIDs&gt;"/> + <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &lt;keepIDs&gt;"/> <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" />