comparison vcfannotate.xml @ 3:28459b837ef8 draft default tip

Uploaded

2:98961914308d

<tool id="vcfannotate" name="VCFannotate:" version="0.0.2">
<requirements>
    <requirement type="package" version="86723982aa">vcflib</requirement>
</requirements>
  <description>Intersect VCF records with BED annotations</description>
  <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
  <inputs>        
    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
    <param name="bed_data" type="data" format="bed" label="BED datasets to itersect with"/>
    <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>

      <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
    </test>
    </tests>
  <help>

Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference sequences in the VCF file. 

-----

.. class:: infomark

3:28459b837ef8

<tool id="vcfannotate" name="VCFannotate:" version="0.0.2">
<requirements>
    <requirement type="package" version="8a5602bf07">vcflib</requirement>
</requirements>
  <description>Intersect VCF records with BED annotations</description>
  <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
  <inputs>        
    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
    <param name="bed_data" type="data" format="bed" label="Select BED dataset to itersect with"/>
    <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>

      <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
    </test>
    </tests>
  <help>

Intersect the records in the VCF file with intervals (features) provided in a BED file. Intersections are done on the reference sequences in the VCF file. 

-----

.. class:: infomark