Mercurial > repos > iuc > bcftools_annotate
changeset 26:bba9853e1fdc 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 07:55:02 +0000 |
| parents | 5f9a85fc49b2 |
| children | |
| files | bcftools_annotate.xml macros.xml |
| diffstat | 2 files changed, 219 insertions(+), 106 deletions(-) [+] |
line wrap: on
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--- a/bcftools_annotate.xml Sun Aug 18 09:38:22 2024 +0000 +++ b/bcftools_annotate.xml Tue Dec 02 07:55:02 2025 +0000 @@ -9,7 +9,6 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $annotation_file = None #set $annotation_hdr = None @@ -175,7 +174,7 @@ <expand macro="macro_include" /> <expand macro="macro_exclude" /> <expand macro="macro_collapse" /> - <expand macro="macro_restrict" /> + <expand macro="macro_region_restrict" /> <expand macro="macro_samples" /> </section> <expand macro="macro_select_output_type" /> @@ -186,10 +185,14 @@ <tests> <test> <param name="input_file" ftype="vcf" value="annotate.vcf" /> - <param name="anno_fmt" value="tab" /> - <param name="annotations" value="annotate.tab" /> - <param name="header_file" value="annotate.hdr" /> - <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="tab" /> + <param name="annotations" value="annotate.tab" /> + <param name="header_file" value="annotate.hdr" /> + </conditional> + <param name="columns" value="CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -218,9 +221,13 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate.vcf" /> - <param name="anno_fmt" value="vcf" /> - <param name="annotations" value="annots.vcf" /> - <param name="columns" value="STR,ID,QUAL,FILTER" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="vcf" /> + <param name="annotations" value="annots.vcf" /> + </conditional> + <param name="columns" value="STR,ID,QUAL,FILTER" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -231,9 +238,13 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate.vcf" /> - <param name="anno_fmt" value="vcf" /> - <param name="annotations" value="annots.bcf" /> - <param name="columns" value="STR,ID,QUAL,FILTER" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="vcf" /> + <param name="annotations" value="annots.bcf" /> + </conditional> + <param name="columns" value="STR,ID,QUAL,FILTER" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -244,9 +255,13 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate2.vcf" /> - <param name="anno_fmt" value="vcf" /> - <param name="annotations" value="annots2.vcf" /> - <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="vcf" /> + <param name="annotations" value="annots2.vcf" /> + </conditional> + <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -257,10 +272,16 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate2.vcf" /> - <param name="anno_fmt" value="vcf" /> - <param name="annotations" value="annots2.vcf" /> - <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> - <param name="samples" value="A" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="vcf" /> + <param name="annotations" value="annots2.vcf" /> + </conditional> + <param name="columns" value="ID,QUAL,FILTER,INFO,FMT" /> + </section> + <section name="sec_restrict"> + <param name="samples" value="A" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -271,8 +292,14 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate3.vcf" /> - <param name="anno_fmt" value="none" /> - <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="none" /> + </conditional> + </section> + <section name="sec_annotate"> + <param name="remove" value="ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -282,8 +309,14 @@ </test> <test> <param name="input_file" ftype="vcf" value="annotate3.vcf" /> - <param name="anno_fmt" value="none" /> - <param name="remove" value="FORMAT" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="none" /> + </conditional> + </section> + <section name="sec_annotate"> + <param name="remove" value="FORMAT" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -294,11 +327,22 @@ <!-- Test region overlap option --> <test> <param name="input_file" ftype="vcf" value="annotate3.vcf" /> - <param name="anno_fmt" value="none" /> - <param name="remove" value="FORMAT" /> + <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="none" /> + </conditional> + </section> + <section name="sec_annotate"> + <param name="remove" value="FORMAT" /> + </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> @@ -312,12 +356,16 @@ <!-- Test min overlap option --> <test> <param name="input_file" ftype="vcf" value="annotate3.vcf" /> - <param name="anno_fmt" value="none" /> - <param name="remove" value="FORMAT" /> - <param name="output_type" value="v" /> <section name="sec_annofile"> + <conditional name="annofile"> + <param name="anno_fmt" value="none" /> + </conditional> <param name="min_overlap" value="0.5"/> </section> + <section name="sec_annotate"> + <param name="remove" value="FORMAT" /> + </section> + <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <not_has_text text="GT:X:PL:Y:AA" /> @@ -366,7 +414,7 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ -@BCFTOOLS_WIKI@ +@BCFTOOLS_HOWTOS@ ]]> </help> <expand macro="citations" />
--- a/macros.xml Sun Aug 18 09:38:22 2024 +0000 +++ b/macros.xml Tue Dec 02 07:55:02 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: