Mercurial > repos > iuc > vcfdistance

diff vcfdistance.xml @ 0:c506b8275b1a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfdistance commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author: iuc
date: Mon, 26 Mar 2018 12:24:06 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfdistance.xml	Mon Mar 26 12:24:06 2018 -0400
@@ -0,0 +1,34 @@
+<tool id="vcfdistance" name="VCFdistance:" version="@WRAPPER_VERSION@+galaxy0">
+  <description>Calculate distance to the nearest variant</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio" />
+  <command>cat "${input1}" | vcfdistance > "${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="vcflib.vcf"/>
+      <output name="out_file1" file="vcfdistance-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Adds a value to each VCF record indicating the distance to the nearest variant in the file.
+
+.. class:: infomark
+
+The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
+
+----
+
+Vcfdistance @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>