Mercurial > repos > iuc > snpsift

diff snpSift_vartype.xml @ 13:ed810da439cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents b884686a80dc
children 80da7fae14b8
line wrap: on
line diff
--- a/snpSift_vartype.xml	Tue Oct 13 17:31:24 2015 -0400
+++ b/snpSift_vartype.xml	Tue Jun 07 09:41:13 2016 -0400
@@ -1,12 +1,14 @@
-<tool id="snpsift_vartype" name="SnpSift Variant Type" version="4.0.0">
+<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0">
     <description>Annotate with variant type</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-        java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2&gt; $log &gt; $output
+    <expand macro="version_command" />
+    <command><![CDATA[
+        java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
@@ -17,7 +19,7 @@
     </outputs>
     <tests>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).
@@ -34,6 +36,8 @@
 .. _MIT license: http://opensource.org/licenses/MIT
 
 @CITATION_SECTION@
+
+]]>
     </help>
     <expand macro="citations" />
 </tool>