diff vcfbreakcreatemulti.xml @ 0:f0dae4ac267e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfbreakcreatemulti.xml	Thu Mar 19 12:43:19 2015 -0400
@@ -0,0 +1,53 @@
+<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3">
+  <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>
+
+   #if str($break_or_create) == "break":
+       vcfbreakmulti "${input1}" > "${out_file1}"
+   #elif str($break_or_create) == "create": 
+       vcfcreatemulti "${input1}" > "${out_file1}"
+   #end if
+
+</command>
+
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+    <param name="break_or_create" type="select" display="radio" label="Break or Create?">
+      <option value="break">Break</option>
+      <option value="create">Create</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="break_or_create" value="break"/>
+      <param name="input1" value="vcflib.vcf"/>
+      <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/>
+    </test>
+    <test>
+      <param name="break_or_create" value="create"/>
+      <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/>
+      <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/>
+    </test>
+  </tests>
+  <help>
+
+This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively):
+
+ - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.
+ - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record.
+
+----
+
+This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+  <expand macro="citations" />
+</tool>