view vcfselectsamples.xml @ 0:88fd8ef7e4af draft

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<tool id="vcfselectsamples" name="VCFselectsamples:" version="0.0.3">
  <description>Select samples from a VCF dataset</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio" />
  <command>vcfkeepsamples "${input1}" ${ ' '.join( map( lambda x:'"%s"' % ( x ), str($vcf_samples ).split(",") ) ) } > "${out_file1}"</command>
  <inputs>
    <param format="vcf" name="input1" type="data" label="Select VCF dataset"  />
    <param name="vcf_samples" type="select" label="Check to keep samples; Uncheck to remove" display="checkboxes" multiple="true">
      <options>
        <filter type="data_meta" ref="input1" key="sample_names" />
      </options>
</param>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="vcf_samples" value="NA00001,NA00003"/>
      <param name="input1" value="vcflib.vcf"/>
      <output name="out_file1" file="vcfselectsamples-test1.vcf"/>
    </test>
   </tests>
  <help>

Allows to keep or remove samples from a VCF file.

-----

.. class:: infomark


**Example**:

Selecting *NA00001* and *NA00003* from the following VCF line::

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00002      NA00003
 20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

will, obviously, remove *NA00002*::

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                              FORMAT      NA00001        NA00003                                                  
 20     1110696 rs6040355 A   G,T 67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2/2:35:4:.,.

----

Vcfselectsamples is based on vcfkeepsamples/vcfremovesamples utilities from **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
</help>
  <expand macro="citations" />
</tool>