diff vcfsort.xml @ 0:433d50620231 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfsort.xml	Thu Mar 19 14:46:40 2015 -0400
@@ -0,0 +1,27 @@
+<tool id="vcfsort" name="VCFsort:" version="0.0.2">
+  <description>Sort VCF dataset by coordinate</description>
+  <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${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="vcfsort-test1-input.vcf"/>
+      <output name="out_file1" file="vcfsort-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
+
+ (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
+
+.. class:: infomark
+
+The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
+
+</help>
+</tool>