view GVF_Features_Extracter.xml @ 3:402c3f0fe807 draft

Uploaded revised vcf_gff.py from Github to fix bug

<?xml version="1.0"?>
<tool id="GVF Features  Extracter_1" name="GVF Feature ID Extracter">
  <description>Extract unique feature IDs from a GVF/GFF3 file </description>
  <command >awk '!/^#/ {print $1":"$2":"$3":"$4}'   $inputgff3File | sort | uniq >  $column_outputfile</command>
  <inputs>
    <param format="gff3" name="inputgff3File" type="data" label="GVF/Gff3 File"/>
  </inputs>
  <outputs>
     <data format="tabular"  name="column_outputfile" />
  </outputs>
<help>

.. class:: infomark

**TIP**

This tool extracts a unique feature identifier from  GVF/GFF3 format, primarily to enable downstream analysis of SNPs or marker design


----

**Example**

*input GFF3*

::

 ##gff-version 3
 1119927 gsMapper        SNP     434     434     .       .       .       ID=1119927:gsMapper:SNP:434;Reference_seq=G;Variant_seq=A;Total_reads=10;Variant_freq=100;Enzyme=AluI;Phase=variant
 1120709 gsMapper        SNP     361     361     .       .       .       ID=1120709:gsMapper:SNP:361;Reference_seq=T;Variant_seq=C;Total_reads=22;Variant_freq=68;Enzyme=TaqI;Phase=variant
 1120709 gsMapper        SNP     704     704     .       .       .       ID=1120709:gsMapper:SNP:704;Reference_seq=A;Variant_seq=G;Total_reads=20;Variant_freq=90;Enzyme=RsaI;Phase=variant

*output tabular text*

::

 1119927:gsMapper:SNP:434
 1120709:gsMapper:SNP:361
 1120709:gsMapper:SNP:704

 -----------------------------------------------------
 
*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum

</help>

</tool>