comparison macros.xml @ 16:2215287d5cc9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

15:86296490704e

<macros>
  <token name="@TOOL_VERSION@">1.10</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="1.10">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.10">samtools</requirement>
  </xml>
  <xml name="matplotlib_requirement">
      <requirement type="package" version="3.4.3">matplotlib</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

<![CDATA[
export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`;
]]>
  </token>
  <xml name="macro_input">
    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
  </xml>
  <token name="@PREPARE_INPUT_FILE@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.is_of_type('vcf')
  bgzip -c '$input_file' > $input_vcf &&
  bcftools index $input_vcf &&
#elif $input_file.is_of_type('vcf_bgzip')
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.tabix_index:
    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
  #else

  <token name="@INPUT_FILE@">
$input_vcf
  </token>

  <xml name="macro_inputs">
    <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
  </xml>
  <token name="@PREPARE_INPUT_FILES@">
<![CDATA[
## May need to symlink input if there is an associated

#for (i, input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.vcf.gz'
  #if $input_file.is_of_type('vcf')
    bgzip -c '$input_file' > $input_vcf &&
    bcftools index $input_vcf &&
  #elif $input_file.is_of_type('vcf_bgzip')
    ln -s '$input_file' $input_vcf &&
    #if $input_file.metadata.tabix_index:
      ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
    #else
      bcftools index $input_vcf &&

        <when value="@TYPE@s_file">
            <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
            <yield />
        </when>        
    </conditional>
  </xml>

  <token name="@PARSE_INTERVALS@">
<![CDATA[
#set $components = []

#end for
#set $intervals_spec = ','.join($components)
]]>
  </token>
  
  <token name="@REGIONS@">
<![CDATA[
#if $section.regions.regions_src == 'regions':
  #set $intervals = $section.regions.regions
  @PARSE_INTERVALS@

    --regions-file '$regions_path'
  #else:
    --regions-file '$section.regions.regions_file'
  #end if
#end if
]]>
  </token>
  
  <token name="@TARGETS@">
<![CDATA[

  @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
]]>
  </token>

  <token name="@PREPARE_REGIONS_FILE@">
<![CDATA[

]]>
  </token>

  <xml name="macro_samples">
      <param argument="--samples" type="text" value="" optional="true" label="Samples"
             help="Comma separated list of samples to annotate (or exclude)">
          <validator type="regex" message="">^(\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" />

  </token>

  <xml name="macro_columns">
    <param name="columns" type="text" value="" optional="true" label="Columns"
            help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
        <validator type="regex" message="COLUMN names  separated by commas">^([^,]+(,[^,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@COLUMNS@">
#if $section.columns != '':
  --columns '${section.columns}'

  </xml>
  <token name="@VCF_IDS@">
${section.vcf_ids}
  </token>

  <token name="@OUTPUT_HELP@">
      <![CDATA[
Output Type
-----------

Output compressed BCF (b), or uncompressed VCF (v).

16:2215287d5cc9

<macros>
  <token name="@TOOL_VERSION@">1.15.1</token>
  <token name="@VERSION_SUFFIX@">0</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>

<![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="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
  </xml>
  <token name="@PREPARE_INPUT_FILE@">
<![CDATA[
## May need to symlink input if there is an associated
#set $input_vcf = 'input.vcf.gz'
#if $input_file.is_of_type('vcf')
  bgzip -c '$input_file' > $input_vcf &&
  bcftools index $input_vcf &&
##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
#elif $input_file.is_of_type('vcf_bgzip')
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.tabix_index:
    ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
  #else

  <token name="@INPUT_FILE@">
$input_vcf
  </token>

  <xml name="macro_inputs">
    <!-- 
    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="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
  </xml>
  <token name="@PREPARE_INPUT_FILES@">
<![CDATA[
## May need to symlink input if there is an associated

#for (i, input_file) in enumerate($input_files):
  #set $input_vcf = 'input' + str($i) + '.vcf.gz'
  #if $input_file.is_of_type('vcf')
    bgzip -c '$input_file' > $input_vcf &&
    bcftools index $input_vcf &&
  ##elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz') -> REQUIRES  https://github.com/galaxyproject/galaxy/pull/14605
  #elif $input_file.is_of_type('vcf_bgzip') or $input_file.is_of_type('vcf.gz')
    ln -s '$input_file' $input_vcf &&
    #if $input_file.metadata.tabix_index:
      ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
    #else
      bcftools index $input_vcf &&

        <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 = []

#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-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[

  @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[

]]>
  </token>

  <xml name="macro_samples">
      <param argument="--samples" type="text" value="" optional="true" label="Samples"
             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" />

  </token>

  <xml name="macro_columns">
    <param name="columns" type="text" value="" optional="true" label="Columns"
            help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
        <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
    </param>
  </xml>
  <token name="@COLUMNS@">
#if $section.columns != '':
  --columns '${section.columns}'

  </xml>
  <token name="@VCF_IDS@">
${section.vcf_ids}
  </token>

<xml name="macro_output_tags">
  <param name="output_tags" argument="--annotate" type="select" optional="true" multiple="True" display="checkboxes" label="Optional tags to output" help="--annotate">
      <yield />
  </param>
</xml>

<xml name="macro_overlap" token_argument="" token_label="">
</xml>


  <token name="@OUTPUT_HELP@">

      <![CDATA[
Output Type
-----------

Output compressed BCF (b), or uncompressed VCF (v).