# HG changeset patch
# User iuc
# Date 1522081733 14400
# Node ID 5b7120c66efcaf3f6732438bc86de1b0a714fbc3
# Parent  a8c5440d69e3f4afb615cb0c90b2b0609e947052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582

diff -r a8c5440d69e3 -r 5b7120c66efc vcfsort.xml
--- a/vcfsort.xml	Mon Oct 03 11:23:06 2016 -0400
+++ b/vcfsort.xml	Mon Mar 26 12:28:53 2018 -0400
@@ -1,23 +1,24 @@
-<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@.0">
-  <description>Sort VCF dataset by coordinate</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command>
-  <inputs>
-    <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="vcfsort-test1-input.vcf"/>
-      <output name="out_file1" file="vcfsort-test1.vcf"/>
-    </test>
+<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0">
+    <description>Sort VCF dataset by coordinate</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command><![CDATA[
+(grep ^"#" "${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>
-
+    <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
@@ -25,6 +26,5 @@
 .. 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>
+    </help>
 </tool>