annotate macros.xml @ 0:1d4c51dcbbbe draft

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<macros>
  <token name="@VERSION@">1.4.0</token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.9">bcftools</requirement>
      <requirement type="package" version="1.9">htslib</requirement>
      <yield />
    </requirements>
  </xml>
  <xml name="citations">
    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <yield />
    </citations>
  </xml>
  <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">
    <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" 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 &&
#elif $input_file.is_of_type('bcf')
  #set $input_vcf = 'input.bcf'
  ln -s '$input_file' $input_vcf &&
  #if $input_file.metadata.bcf_index:
    ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
  #else
    bcftools index $input_vcf &&
  #end if
#elif $input_file.is_of_type('bcf_bgzip')
  ln -s '$input_file' $input_vcf &&
#end if
]]>
  </token>
  <token name="@INPUT_FILE@">
$input_vcf
  </token>
  <xml name="macro_select_output_type">
    <param name="output_type" type="select">
      <option value="b">compressed BCF</option>
      <option value="u">uncompressed BCF</option>
      <option value="z">compressed VCF</option>
      <option value="v">uncompressed VCF</option>
    </param>
  </xml>
  <token name="@OUTPUT_TYPE@">
#if str($output_type) != "__none__":
  --output-type '${output_type}'
#end if
  </token>

  <xml name="macro_vcf_output">
      <data name="output_file" format="vcf">
        <change_format>
          <when input="output_type" value="b" format="bcf" />
          <when input="output_type" value="u" format="bcf" />
          <when input="output_type" value="z" format="vcf_bgzip" />
          <when input="output_type" value="v" format="vcf" />
        </change_format>
      </data>
  </xml>

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

Output compressed BCF (b), or uncompressed VCF (v).
Use the BCF option when piping between bcftools subcommands to speed up
performance by removing unecessary compression/decompression
and VCF<->BCF conversion.

This Galaxy tool recommends using the compressed BCF format
as piping is not implemented, and uncompressed data would
use unnecessary amounts of space.
  ]]></token>
</macros>