diff vcfdistance.xml @ 0:6e0fc18309f4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfdistance.xml	Thu Mar 19 14:26:53 2015 -0400
@@ -0,0 +1,34 @@
+<tool id="vcfdistance" name="VCFdistance:" version="0.0.3">
+  <description>Calculate distance to the nearest variant</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <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>