comparison macros.xml @ 5:53a667173f9c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

4:5272100dd270

<macros>
  <token name="@VERSION@">1.3.1</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.3.1">bcftools</requirement>
      <!-- conda dependency -->
      <requirement type="package" version="1.3.2">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

      <option value="v">uncompressed VCF</option>
    </param>
  </xml>
  <token name="@OUTPUT_TYPE@">
#if str($output_type) != "__none__":
  --output-type "${output_type}"
#end if
  </token>

  <xml name="macro_vcf_output">
      <data name="output_file" format="vcf">

        <when value="regions_file">
            <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
        </when>
    </conditional>
  </xml>
  <token name="@REGIONS@">
#if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
  --regions '$section.regions.regions'
#elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
  --regions-file '$section.regions.regions_file'
#end if
  </token>

  <xml name="macro_targets_file">
            <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
              <yield/>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />

]]>
  </token>

  <xml name="macro_samples">
      <param name="samples" type="text" value="" label="Samples" optional="true"
             help="(-s) comma separated list of samples to annotate (or exclude with &quot;^&quot; prefix)">
          <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" />
      <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
             help="(-S) 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>

5:53a667173f9c

<macros>
  <token name="@VERSION@">1.4.0</token>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.4">bcftools</requirement>
      <requirement type="package" version="1.4">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="samtools_requirement">
      <requirement type="package" version="1.3.1">samtools</requirement>
  </xml>
  <xml name="version_command">
    <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
  </xml>

      <option value="v">uncompressed VCF</option>
    </param>
  </xml>
  <token name="@OUTPUT_TYPE@">
#if str($output_type) != "__none__":
  --output-type '${output_type}'
#end if
  </token>

  <xml name="macro_vcf_output">
      <data name="output_file" format="vcf">

        <when value="regions_file">
            <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
        </when>
    </conditional>
  </xml>
  <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
#end if
]]>
  </token>
  <token name="@REGIONS@">
#if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
  --regions '$section.regions.regions'
#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
  </token>
  <xml name="macro_targets_file">
            <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
              <yield/>
            </param>
            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />

]]>
  </token>

  <xml name="macro_samples">
      <param name="samples" type="text" value="" label="Samples" optional="true"
             help="(-s) 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 name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
             help="(-S) 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>