<tool id="vcf_filter" name="Filter" version="1.0.0">
  <description>a VCF file</description>
  <command interpreter="python">
    vcfPytools.py
      filter 
      --in=$input1
      --out=$output1
      --quality=$quality
      #for $i in $info_filter:
        --info ${i.info}
      #end for
      $remove_genotypes
      $mark_as_pass
  </command>
  <inputs>
    <param name="input1" label="VCF file" type="data" format="vcf" />
    <param name="quality" label="Filter by quality" type="integer" value='' help="Filter out SNPs with qualities lower than selected value" />
    <repeat name="info_filter" title="Filter based on entries in the info string">
      <param name="info" label="Filter" type="text" value='' help='This option takes three values: the info string tag, the cutoff value and whether to filter out those records with less than (lt) or greater than (gt) this value.  For example: DP 10 lt ' />
    </repeat>
    <param name="remove_genotypes" label="Remove the genotype strings" type="boolean" truevalue="--remove-genotypes" falsevalue="" checked="False" />
    <param name="mark_as_pass" label="Mark all records as having passed filters" type="boolean" truevalue="--mark-as-pass" falsevalue="" checked="False" />
  </inputs>
  <tests>
    <test>
      <param name="input1" value="test.small.vcf" ftype="vcf" />
      <param name="quality" value="9" />
      <param name="info" value="NS 360 gt"/>
      <param name="remove_genotypes" value="" />
      <param name="mark_as_pass" value="" />
      <output name="output" file="test_filter_quality_9_NS_360_gt.vcf" lines_diff="6" ftype="vcf" />
    </test>
    <test>
      <param name="input1" value="test.small.vcf" ftype="vcf" />
      <param name="quality" value="9" />
      <param name="info" value="DP 2000 lt"/>
      <param name="remove_genotypes" value="" />
      <param name="mark_as_pass" value="" />
      <output name="output" file="test_filter_quality_9_DP_2000_lt.vcf" lines_diff="6" ftype="vcf" />
    </test>
  </tests>
  <outputs>
    <data format="vcf" name="output1" label="${tool.name} ${on_string}" />
  </outputs>
  <help>

**What it does**

This tool uses vcfPytools_' filter command

.. _vcfPytools: https://github.com/AlistairNWard/vcfPytools

Quality option will check the variant quality for each record and if it is below the defined value, the filter field will be populated with the filter entry Q[value].

Any value in the info string can be used for filtering by using the 'Filter by info' option.  This option takes three values: the info string tag, the cutoff value and whether to filter out those records with less than (lt) or greater than (gt) this value.  For example:

  DP 10 lt 

would filter out all varianta with a depth (DP) less than 10 and the filter field would be populated with DP10.

This option can be defined as many times as required.

  </help>
</tool>