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diff vcfflatten.xml @ 0:ac725e729ac6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfflatten commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:32:13 -0500
parents
children 5fe607441f62
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfflatten.xml	Mon Nov 09 12:32:13 2015 -0500
@@ -0,0 +1,30 @@
+<tool id="vcfflatten2" name="VCFflatten:" version="0.0.3">
+  <description>Removes multi-allelic sites by picking the most common alternate</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio" />
+  <command>vcfflatten "${input1}" > "${out_file1}"</command>
+  <inputs>
+    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="vcfflatten-input1.vcf"/>
+      <output name="out_file1" file="vcfflatten-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Removes multi-allelic sites by picking the most common alternate.  Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.
+
+----
+
+Vcfflatten @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>