diff vcfallelicprimitives.xml @ 0:239da20770dc

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfallelicprimitives.xml	Wed Jun 11 17:10:38 2014 -0400
@@ -0,0 +1,41 @@
+<tool id="vcfallelicprimitives" name="VcfAllelicPrimitives:" version="0.0.1">
+<requirements>
+    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
+</requirements>
+  <description>Split alleleic primitives (gaps or mismatches) into multiple VCF lines</description>
+  <command>cat "${input}" | vcfallelicprimitives ${m_option} -t "${t_option}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
+    <param name="m_option" type="boolean" checked="true" truevalue="-m" falsevalue="" label="Retain MNPs as separate events" help="--use-mnps option"/>
+    <param name="t_option" size="20" type="text" value="Split primitives" label="Mark records which are split with this tag" help="--tag-parsed option"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="m_option" value="true"/>
+      <param name="t_option" value="Split primitives"/>
+      <param name="input" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfallelicprimitives-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, this tools splits the record into multiple lines, but drops all INFO fields.  "Pure" MNPs are split into multiple SNPs unless the -m flag is provided.  Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.
+
+The options are::
+                                                                                                                           
+    --use-mnps (-m)
+    Retain MNPs as separate events                                                                          
+    
+    --tag-parsed (-t) FLAG
+    Tag records which are split apart of a complex allele                                                                                                                                                             
+    with this flag                                                 
+
+----
+
+Vcfallelicprimitives is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+</tool>