Mercurial > repos > iuc > bcftools_csq
changeset 18:9f69e7d58d03 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 08:13:25 +0000 |
| parents | d237eaef451f |
| children | |
| files | bcftools_csq.xml macros.xml |
| diffstat | 2 files changed, 242 insertions(+), 130 deletions(-) [+] |
line wrap: on
line diff
--- a/bcftools_csq.xml Sun Aug 18 10:00:41 2024 +0000 +++ b/bcftools_csq.xml Tue Dec 02 08:13:25 2025 +0000 @@ -4,13 +4,12 @@ <token name="@EXECUTABLE@">csq</token> <import>macros.xml</import> </macros> - <expand macro="bio_tools" /> + <expand macro="bio_tools"/> <expand macro="requirements"> <expand macro="samtools_requirement"/> </expand> - <expand macro="version_command" /> + <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_required.reference_source @PREPARE_FASTA_REF@ @@ -40,6 +39,9 @@ #if str($sec_csq_opts.trim_protein_seq) --trim-protein-seq $sec_csq_opts.trim_protein_seq #end if +#if $sec_csq_opts.genetic_code + --genetic-code '$sec_csq_opts.genetic_code' +#end if ## Subset section #set $section = $sec_subset @@ -61,104 +63,149 @@ ]]> </command> <inputs> - <expand macro="macro_input" /> + <expand macro="macro_input"/> <section name="sec_required" expanded="true" title="Required References"> - <expand macro="macro_fasta_ref" /> - <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" - help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/> + <expand macro="macro_fasta_ref"/> + <param name="gff_annot" type="data" format="gff3" label="GFF3 annotation file" help="From Ensembl: ftp://ftp.ensembl.org/pub/current_gff3/"/> </section> <section name="sec_csq_opts" expanded="true" title="CSQ Options"> - <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" - help="-ncsq 16"/> - <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" - help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/> - <param name="phase" type="select" optional="true" label="phase" - help="how to construct haplotypes and how to deal with unphased data"> - <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option> - <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option> + <param name="ncsq" type="integer" value="16" min="1" max="50" label="maximum number of consequences to consider per site" help="-ncsq 16"/> + <param name="local_csq" type="boolean" truevalue="--local-csq" falsevalue="" checked="false" label="run localized predictions considering only one VCF record at a time" help="--local-csq switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time"/> + <param name="phase" type="select" optional="true" label="phase" help="how to construct haplotypes and how to deal with unphased data"> + <option value="a">take GTs as is, create haplotypes regardless of phase (0/1 -> 0|1)</option> + <option value="m">merge *all* GTs into a single haplotype (0/1 -> 1, 1/2 -> 1)</option> <option value="r">require phased GTs, throw an error on unphased het GTs</option> - <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option> + <option value="R">create non-reference haplotypes if possible (0/1 -> 1|1, 1/2 -> 1|2)</option> <option value="s">skip unphased GTs</option> </param> - <param name="custom_tag" type="text" value="" optional="true" - label="use this custom tag to store consequences rather than the default BCSQ tag"> - <validator type="regex" message="">^(\w+)?$</validator> + <param name="custom_tag" type="text" value="" optional="true" label="use this custom tag to store consequences rather than the default BCSQ tag"> + <validator type="regex" message="">^(\w+)?$</validator> </param> - <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" - help="Abbreviate protein-changing predictions to max INT aminoacids" /> + <param argument="--trim-protein-seq" type="integer" min="0" value="" optional="true" label="Abbreviate protein-changing predictions" help="Abbreviate protein-changing predictions to max INT aminoacids"/> + <param argument="--genetic-code" type="select" optional="true" label="Genetic code table" help="Choose a predefined genetic code table used to translate coding sequences. Leave unset for the default bcftools behaviour."> + <option value="0">0: Standard simplified</option> + <option value="1">1: Standard</option> + <option value="2">2: Vertebrate mitochondrial</option> + <option value="3">3: Yeast mitochondrial</option> + <option value="4">4: Mold, Protozoan, Coelenterate mitochondrial; Mycoplasma; Spiroplasma</option> + <option value="5">5: Invertebrate mitochondrial</option> + <option value="6">6: Ciliate, Dasycladacean and Hexamita nuclear</option> + <option value="9">9: Echinoderm and Flatworm mitochondrial</option> + <option value="10">10: Euplotid nuclear</option> + <option value="11">11: Bacterial, Archaeal and Plant plastid</option> + <option value="12">12: Alternative yeast nuclear</option> + <option value="13">13: Ascidian mitochondrial</option> + <option value="14">14: Alternative flatworm mitochondrial</option> + <option value="15">15: Blepharisma nuclear</option> + <option value="16">16: Chlorophycean mitochondrial</option> + <option value="21">21: Trematode mitochondrial</option> + <option value="22">22: Scenedesmus obliquus mitochondrial</option> + <option value="23">23: Thraustochytrium mitochondrial</option> + <option value="24">24: Pterobranchia mitochondrial</option> + <option value="25">25: Candidate Division SR1 and Gracilibacteria</option> + <option value="26">26: Pachysolen tannophilus nuclear</option> + <option value="27">27: Karyorelict nuclear</option> + <option value="28">28: Condylostoma nuclear</option> + <option value="29">29: Mesodinium nuclear</option> + <option value="30">30: Peritrich nuclear</option> + <option value="31">31: Blastocrithidia nuclear</option> + <option value="33">33: Cephalodiscidae mitochondrial UAA-Tyr</option> + </param> </section> - <section name="sec_restrict" expanded="false" title="Restrict to"> - <expand macro="macro_restrict" /> - <expand macro="macro_restrict" type="target" label_type="Target" /> - <expand macro="macro_include" /> - <expand macro="macro_exclude" /> + <expand macro="macro_region_restrict"/> + <expand macro="macro_target_restrict"/> + <expand macro="macro_include"/> + <expand macro="macro_exclude"/> </section> <section name="sec_subset" expanded="false" title="Subset Options"> - <expand macro="macro_samples" /> + <expand macro="macro_samples"/> </section> - <expand macro="macro_select_output_type" /> + <expand macro="macro_select_output_type"/> </inputs> <outputs> - <expand macro="macro_vcf_output" /> + <expand macro="macro_vcf_output"/> </outputs> <tests> <test> - <param name="input_file" ftype="vcf" value="csq.vcf" /> - <expand macro="test_using_reference" ref="csq.fa" /> - <param name="gff_annot" ftype="gff3" value="csq.gff3" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="csq.vcf"/> + <section name="sec_required"> + <expand macro="test_using_reference" ref="csq.fa"/> + </section> + <section name="sec_required"> + <param name="gff_annot" ftype="gff3" value="csq.gff3"/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text text="BCSQ" /> + <has_text text="BCSQ"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="csq.vcf" /> - <expand macro="test_using_reference" select_from="cached" ref="csq" /> - <param name="gff_annot" ftype="gff3" value="csq.gff3" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="csq.vcf"/> + <section name="sec_required"> + <expand macro="test_using_reference" select_from="cached" ref="csq"/> + </section> + <section name="sec_required"> + <param name="gff_annot" ftype="gff3" value="csq.gff3"/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text text="BCSQ" /> + <has_text text="BCSQ"/> </assert_contents> </output> </test> <!-- Test protein seq prediction--> <test> - <param name="input_file" ftype="vcf" value="csq.vcf" /> - <expand macro="test_using_reference" select_from="cached" ref="csq" /> - <param name="gff_annot" ftype="gff3" value="csq.gff3" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="csq.vcf"/> + <section name="sec_required"> + <expand macro="test_using_reference" select_from="cached" ref="csq"/> + </section> + <section name="sec_required"> + <param name="gff_annot" ftype="gff3" value="csq.gff3"/> + </section> + <param name="output_type" value="v"/> <section name="sec_csq_opts"> <param name="trim_protein_seq" value="10"/> + <param name="genetic_code" value="1"/> </section> <output name="output_file"> <assert_contents> - <has_text text="BCSQ" /> + <has_text text="BCSQ"/> </assert_contents> </output> <assert_command> - <has_text text="--trim-protein-seq" /> + <has_text text="--trim-protein-seq"/> + <has_text text="--genetic-code '1'"/> </assert_command> </test> <!-- Test region overlap--> <test> - <param name="input_file" ftype="vcf" value="csq.vcf" /> - <expand macro="test_using_reference" select_from="cached" ref="csq" /> - <param name="gff_annot" ftype="gff3" value="csq.gff3" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="csq.vcf"/> + <section name="sec_required"> + <expand macro="test_using_reference" select_from="cached" ref="csq"/> + </section> + <section name="sec_required"> + <param name="gff_annot" ftype="gff3" value="csq.gff3"/> + </section> + <param name="output_type" value="v"/> <section name="sec_restrict"> - <param name="regions_overlap" value="1"/> + <conditional name="regions"> + <param name="regions_src" value="regions" /> + <repeat name="region_specs"> + <param name="chrom" value="1" /> + </repeat> + </conditional> </section> <output name="output_file"> <assert_contents> - <has_text text="BCSQ" /> + <has_text text="BCSQ"/> </assert_contents> </output> <assert_command> - <has_text text="--regions-overlap" /> + <has_text text="--regions-overlap"/> </assert_command> </test> </tests> @@ -197,8 +244,8 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ -@BCFTOOLS_WIKI@ +@BCFTOOLS_HOWTOS@ ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>
--- a/macros.xml Sun Aug 18 10:00:41 2024 +0000 +++ b/macros.xml Tue Dec 02 08:13:25 2025 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">1.15.1</token> - <token name="@VERSION_SUFFIX@">4</token> - <token name="@PROFILE@">20.01</token> + <token name="@TOOL_VERSION@">1.22</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">24.1</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">bcftools</xref> @@ -10,15 +10,15 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> - <requirement type="package" version="1.15.1">htslib</requirement> + <requirement type="package" version="1.22.1">htslib</requirement> <yield /> </requirements> </xml> <xml name="samtools_requirement"> - <requirement type="package" version="1.15.1">samtools</requirement> + <requirement type="package" version="1.22.1">samtools</requirement> </xml> <xml name="matplotlib_requirement"> - <requirement type="package" version="3.5.3">matplotlib</requirement> + <requirement type="package" version="3.10.7">matplotlib</requirement> </xml> <xml name="version_command"> <version_command>bcftools 2>&1 | grep 'Version:'</version_command> @@ -30,16 +30,11 @@ <yield /> </citations> </xml> - <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token> - <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token> + <token name="@BCFTOOLS_HOWTOS@">https://samtools.github.io/bcftools/howtos/index.html</token> + <token name="@BCFTOOLS_MANPAGE@">https://www.htslib.org/doc/bcftools.html</token> <token name="@THREADS@"> --threads \${GALAXY_SLOTS:-4} </token> - <token name="@PREPARE_ENV@"> -<![CDATA[ -export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; -]]> - </token> <xml name="macro_input"> <!-- REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files @@ -294,8 +289,8 @@ help="inverts the query/filtering applied by the targets" /> </xml> - <xml name="macro_restriction_spec" token_type="region" token_label_type="Region"> - <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1"> + <xml name="macro_restriction_spec" tokens="type,label_type"> + <repeat name="@TYPE@_specs" title="@LABEL_TYPE@ Filter" default="1" min="1"> <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome"> <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator> </param> @@ -305,36 +300,85 @@ <param name="stop" type="text" label="@LABEL_TYPE@ end position"> <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> </param> - <yield /> </repeat> </xml> - <xml name="macro_restrictions_file" token_type="region" token_label_type="Region"> + <xml name="macro_restrictions_file" tokens="type,label_type"> <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" /> </xml> - <xml name="macro_restrict" token_type="region" token_label_type="Region" > + <xml name="__macro_restrict__" tokens="type,label_select,label_type,pos_is_default,rec_is_default"> <conditional name="@TYPE@s"> - <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s"> - <option value="__none__">Do not restrict to @LABEL_TYPE@s</option> - <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option> - <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option> + <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@"> + <option value="__none__">Do not restrict to @LABEL_TYPE@s</option> + <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option> + <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option> + </param> + <when value="__none__"/> + <when value="@TYPE@s"> + <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" /> + <yield /> + <param argument="--@TYPE@s-overlap" type="select" label="Consider variant calls with partial overlap with @LABEL_TYPE@(s) if ..." help="Set to 0 if the record has to have POS inside a region; set to 1 if also overlapping records with POS outside a region should be included (this includes indels with POS at the end of a region, which are technically outside the region); or set to 2 to include only true overlapping variation (compare the full VCF representation 'TA>T-' vs the true sequence variation 'A>-')."> + <option value="0" selected="@POS_IS_DEFAULT@">0: the variant's POS falls in the region</option> + <option value="1" selected="@REC_IS_DEFAULT@">1: any part of the variant's representation overlaps the region</option> + <option value="2">2: the variant's actual sequence change falls in the region</option> + </param> + </when> + <when value="@TYPE@s_file"> + <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> + <yield /> + <param argument="--@TYPE@s-overlap" type="select" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)"> + <option value="0" selected="@POS_IS_DEFAULT@">0: POS in the region</option> + <option value="1" selected="@REC_IS_DEFAULT@">1: Record overlaps</option> + <option value="2">2: Variant overlaps</option> </param> - <when value="__none__"/> - <when value="@TYPE@s"> - <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" /> - <yield /> - </when> - <when value="@TYPE@s_file"> - <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> - <yield /> - </when> + </when> + </conditional> + </xml> + + <xml name="__macro_restrict_simple__" tokens="type,label_select,label_type"> + <conditional name="@TYPE@s"> + <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@"> + <option value="__none__">Do not restrict to @LABEL_TYPE@s</option> + <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option> + <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option> + </param> + <when value="__none__"/> + <when value="@TYPE@s"> + <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" /> + <yield /> + </when> + <when value="@TYPE@s_file"> + <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> + <yield /> + </when> </conditional> - <param argument="--@TYPE@s-overlap" type="select" optional="true" label="@LABEL_TYPE@ overlap" help="Include if POS in the region (0), record overlaps (1), variant overlaps (2)"> - <option value="0">0: POS in the region</option> - <option value="1">1: Record overlaps</option> - <option value="2">2: Variant overlaps</option> - </param> + </xml> + + <xml name="macro_region_restrict" token_label_select="Regions"> + <expand macro="__macro_restrict__" type="region" label_select="@LABEL_SELECT@" label_type="Region" pos_is_default="false" rec_is_default="true" /> + </xml> + + <xml name="macro_region_restrict_simple" token_label_select="Regions"> + <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup? --> + <expand macro="__macro_restrict_simple__" type="region" label_select="@LABEL_SELECT@" label_type="Region" /> + </xml> + + <xml name="macro_target_restrict"> + <expand macro="__macro_restrict__" type="target" label_select="Target" label_type="Target" pos_is_default="true" rec_is_default="false"> + <expand macro="macro_invert_targets" /> + </expand> + </xml> + + <xml name="macro_target_restrict_simple"> + <!-- To be used with subcommands that don't support the 'regions-overlap' option. Currently only mpileup and call? --> + <expand macro="__macro_restrict_simple__" type="target" label_select="Target" label_type="Target"> + <expand macro="macro_invert_targets" /> + </expand> + </xml> + + <xml name="macro_mask_restrict"> + <expand macro="__macro_restrict__" type="mask" label_select="Mask" label_type="Mask" pos_is_default="false" rec_is_default="true" /> </xml> <token name="@PARSE_INTERVALS@"> @@ -345,7 +389,7 @@ #set $start = str($i.start).strip() #set $stop = str($i.stop).strip() #if $start or $stop: - $components.append($chrom + ':' + ($start or '0') + '-' + $stop) + $components.append($chrom + ':' + ($start or '1') + '-' + $stop) #else: $components.append($chrom) #end if @@ -357,18 +401,14 @@ <token name="@MASK@"> <![CDATA[ #if $section.conditional_soft_filter.selector == 'enabled' and $section.conditional_soft_filter.soft_filter - #if $section.conditional_soft_filter.masks.masks_src == 'regions': - #set $intervals = $section.conditional_soft_filter.masks.masks - @PARSE_INTERVALS@ - --mask '$intervals_spec' - #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file' and $section.conditional_soft_filter.masks.masks_file: - #if $masks_path is not None: - --mask-file '$masks_path' - #else: + #if $section.conditional_soft_filter.masks.masks_src != '__none__': + #if $section.conditional_soft_filter.masks.masks_src == 'masks': + #set $intervals = $section.conditional_soft_filter.masks.mask_specs + @PARSE_INTERVALS@ + --mask '$intervals_spec' + #elif $section.conditional_soft_filter.masks.masks_src == 'masks_file': --mask-file '$section.conditional_soft_filter.masks.masks_file' #end if - #end if - #if $section.conditional_soft_filter.masks_overlap --mask-overlap $section.conditional_soft_filter.masks_overlap #end if #end if @@ -378,37 +418,42 @@ <token name="@REGIONS@"> <![CDATA[ -#if $section.regions.regions_src == 'regions': - #set $intervals = $section.regions.regions - @PARSE_INTERVALS@ - --regions '$intervals_spec' -#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: - #if $regions_path is not None: - --regions-file '$regions_path' - #else: - --regions-file '$section.regions.regions_file' +#if $section.regions.regions_src != '__none__': + #if $section.regions.regions_src == 'regions': + #set $intervals = $section.regions.region_specs + @PARSE_INTERVALS@ + --regions '$intervals_spec' + #elif $section.regions.regions_src == 'regions_file': + #if $regions_path is not None: + --regions-file '$regions_path' + #else: + --regions-file '$section.regions.regions_file' + #end if + #end if + #if 'regions_overlap' in $section.regions: + --regions-overlap $section.regions.regions_overlap #end if #end if -#if $section.regions_overlap - --regions-overlap $section.regions_overlap -#end if - ]]> </token> <token name="@TARGETS@"> <![CDATA[ -#if $targets_path: - --targets-file "${section.targets.invert_targets_file}${targets_path}" -#elif $section.targets.targets_src == 'targets': - #set $intervals = $section.targets.targets - @PARSE_INTERVALS@ - --targets '${section.targets.invert_targets_file}$intervals_spec' -#elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: - --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" -#end if -#if $section.targets_overlap - --targets-overlap $section.targets_overlap +#if $section.targets.targets_src != '__none__': + #if $section.targets.targets_src == 'targets': + #set $intervals = $section.targets.target_specs + @PARSE_INTERVALS@ + --targets '${section.targets.invert_targets_file}$intervals_spec' + #elif $section.targets.targets_src == 'targets_file': + #if $targets_path: + --targets-file '${section.targets.invert_targets_file}${targets_path}' + #else: + --targets-file '${section.targets.invert_targets_file}${section.targets.targets_file}' + #end if + #end if + #if 'targets_overlap' in $section.targets: + --targets-overlap $section.targets.targets_overlap + #end if #end if ]]> </token> @@ -417,7 +462,7 @@ <![CDATA[ #set $regions_path = None #if 'regions' in $section - #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: + #if $section.regions.regions_src == 'regions_file': #if $section.regions.regions_file.ext.startswith('bed'): #set $regions_path = 'regions_file.bed' ln -s '$section.regions.regions_file' $regions_path && @@ -461,11 +506,31 @@ </param> <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" /> - <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" - help="File of samples to include" /> + <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" help="File of samples to include" /> <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file" help="inverts the query/filtering applied by Samples file" /> </xml> + + <xml name="macro_samples_enhanced" token_all_samples="" token_file_help="File listing samples to include one per line."> + <conditional name="specify_samples"> + <param name="how" type="select" label="How do you want to select samples?"> + <option value="-s">Specify samples manually</option> + <option value="-S">Provide sample file</option> + <option value="@ALL_SAMPLES@" selected="true">No selection; just use all samples found in input</option> + </param> + <when value="-s"> + <param argument="--samples" name="samples_spec" type="text" optional="false" label="Sample(s)" help="Specify a single sample by name or a comma-separated list of sample names."> + <validator type="expression" message="Please specify a single sample by name or a comma-separated list of sample names">value.strip() and value[0] not in "^," and ",," not in value</validator> + </param> + <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude these samples instead of including them?" help="Equivalent to prefixing the list of samples with "^" on the command line."/> + </when> + <when value="-S"> + <param argument="--samples_file" type="data" format="tabular" optional="@IS_OPTIONAL@" label="Samples file" help="@FILE_HELP@" /> + <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude the samples listed in the file instead of including them?" help="Equivalent to prefixing the file with "^" on the command line."/> + </when> + <when value="@ALL_SAMPLES@" /> + </conditional> + </xml> <token name="@SAMPLES@"> #set $samples_defined = False #if str($section.samples) != '': @@ -478,8 +543,8 @@ #end if </token> - <xml name="macro_sample"> - <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" /> + <xml name="macro_sample" token_help="Apply variants of the given sample"> + <param name="sample" type="text" optional="true" label="Sample" help="@HELP@" /> </xml> <token name="@SAMPLE@"> #if $section.sample: