comparison vcfannotate.xml @ 1:e756415c3a9f draft default tip

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0:911df9fc9512

<requirements>
    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">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 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"/>
    <param format="vcf" name="input" type="data" label="From"/>
  </inputs>
  <outputs>
    <data format="vcf" name="out_file1" />
  </outputs>
  <tests>

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                                                                                       FORMAT      NA00001        NA00002      NA00003                                                  
 20     1110696 rs6040355 A   G,T 67   PASS   AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

----

Vcfannotate is a part of **VCFlib** toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 


</help>
</tool>

1:e756415c3a9f

<requirements>
    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">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>
  <tests>

 #CHROM POS     ID        REF ALT QUAL FILTER INFO                                                                                       FORMAT      NA00001        NA00002      NA00003                                                  
 20     1110696 rs6040355 A   G,T 67   PASS   AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.

----

Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 


</help>
</tool>