comparison macros.xml @ 23:793ae03deb13 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc

22:8b260d252ff4

<macros>
  <token name="@TOOL_VERSION@">1.15.1</token>
  <token name="@VERSION_SUFFIX@">4</token>
  <token name="@PROFILE@">20.01</token>
  <xml name="bio_tools">
      <xrefs>
          <xref type="bio.tools">bcftools</xref>
      </xrefs>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
      <requirement type="package" version="1.15.1">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.15.1">samtools</requirement>
  </xml>
  <xml name="matplotlib_requirement">
      <requirement type="package" version="3.5.3">matplotlib</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <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="@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
    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />

    <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
    label="Invert Targets"
    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">
        <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>
        <param name="start" type="text" label="@LABEL_TYPE@ start position">
            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
        </param>
        <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">
    <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" >
    <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>
        <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>

  <token name="@PARSE_INTERVALS@">
<![CDATA[
#set $components = []
#for $i in $intervals:
  #set $chrom = str($i.chrom).strip()
  #set $start = str($i.start).strip()
  #set $stop = str($i.stop).strip()
  #if $start or $stop:
    $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)

  </token>
  
  <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:
      --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

]]>
  </token>

  <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'
  #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
#end if
]]>
  </token>

  <token name="@PREPARE_REGIONS_FILE@">
<![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_file.ext.startswith('bed'):
      #set $regions_path = 'regions_file.bed'
      ln -s '$section.regions.regions_file' $regions_path &&
    #end if
  #end if

             help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
          <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
      </param>
      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
             help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
      <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>
  <token name="@SAMPLES@">
#set $samples_defined = False
#if str($section.samples) != '':
  #set $samples_defined = True

  #set $samples_defined = True
  --samples-file "${section.invert_samples_file}${section.samples_file}"
#end if
  </token>

  <xml name="macro_sample">
      <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
  </xml>
  <token name="@SAMPLE@">
#if $section.sample:
  --sample '${section.sample}'
#end if

23:793ae03deb13

<macros>
  <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>
      </xrefs>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
      <requirement type="package" version="1.22.1">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.22.1">samtools</requirement>
  </xml>
  <xml name="matplotlib_requirement">
      <requirement type="package" version="3.10.7">matplotlib</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <yield />
    </citations>
  </xml>
  <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>
  <xml name="macro_input">
    <!-- 
    REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files
    <param name="input_files" type="data" format="vcf,vcf.gz,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />

    <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
    label="Invert Targets"
    help="inverts the query/filtering applied by the targets" />
  </xml>

  <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>
        <param name="start" type="text" label="@LABEL_TYPE@ start position">
            <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
        </param>
        <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>
    </repeat>
  </xml>

  <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__" 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_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>
    </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>
  </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@">
<![CDATA[
#set $components = []
#for $i in $intervals:
  #set $chrom = str($i.chrom).strip()
  #set $start = str($i.start).strip()
  #set $stop = str($i.stop).strip()
  #if $start or $stop:
    $components.append($chrom + ':' + ($start or '1') + '-' + $stop)
  #else:
    $components.append($chrom)
  #end if
#end for
#set $intervals_spec = ','.join($components)

  </token>
  
  <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 != '__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
    --mask-overlap $section.conditional_soft_filter.masks_overlap
  #end if
#end if

]]>
  </token>

  <token name="@REGIONS@">
<![CDATA[
#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
]]>
  </token>
  
  <token name="@TARGETS@">
<![CDATA[
#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>

  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[
#set $regions_path = None
#if 'regions' in $section
  #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 &&
    #end if
  #end if

             help="Comma-separated list of samples to annotate (or exclude) or - to include all samples">
          <validator type="regex" message="Comma-separated list of samples or - to include all samples">^(-|\w+(,\w+)*)?$</validator>
      </param>
      <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
             help="Inverts the query/filtering applied by Samples (adds &quot;^&quot; prefix to exclude)" />
      <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 &quot;^&quot; 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 &quot;^&quot; on the command line."/>
          </when>
          <when value="@ALL_SAMPLES@" />
      </conditional>
  </xml>
  <token name="@SAMPLES@">
#set $samples_defined = False
#if str($section.samples) != '':
  #set $samples_defined = True

  #set $samples_defined = True
  --samples-file "${section.invert_samples_file}${section.samples_file}"
#end if
  </token>

  <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 $section.sample:
  --sample '${section.sample}'
#end if