# HG changeset patch
# User iuc
# Date 1465308320 14400
# Node ID 0af41de4eda1ff0dc0ed1e3874736742d7e4bd74
# Parent  9e6fa49c107796608b19a14715f5d750f7815bec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31

diff -r 9e6fa49c1077 -r 0af41de4eda1 snpSift_geneSets.xml
--- a/snpSift_geneSets.xml	Thu Jan 22 08:58:01 2015 -0500
+++ b/snpSift_geneSets.xml	Tue Jun 07 10:05:20 2016 -0400
@@ -1,21 +1,23 @@
-<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0">
+<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
     <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
     <!-- 
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
-    <command>
-        java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v
         #if $db_opts.db_opts_selector == "db"
           "${db_opts.database.fields.path}"
         #elif $db_opts.db_opts_selector == "histdb"
           "$db_opts.histdb"
         #end if
-        
-        $input 2&gt; $log &gt; $output
+        "$input" 2> "$log" > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -39,10 +41,9 @@
         <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
         <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
     </tests>
-    <help>
+    <help><![CDATA[
 This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome.
 
 .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets
@@ -60,6 +61,8 @@
 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
 .. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550
 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545
+
+]]>
     </help>
     <expand macro="citations">
         <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
diff -r 9e6fa49c1077 -r 0af41de4eda1 snpSift_macros.xml
--- a/snpSift_macros.xml	Thu Jan 22 08:58:01 2015 -0500
+++ b/snpSift_macros.xml	Tue Jun 07 10:05:20 2016 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.0">snpEff</requirement>
+            <requirement type="package" version="4.1">snpEff</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,6 +10,10 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <xml name="version_command">
+    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
+  </xml>
+  <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
 
 For details about this tool, please go to:
diff -r 9e6fa49c1077 -r 0af41de4eda1 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 22 08:58:01 2015 -0500
+++ b/tool_dependencies.xml	Tue Jun 07 10:05:20 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="snpEff" version="4.0">
-        <repository changeset_revision="6bc55957927b" name="package_snpeff_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="snpEff" version="4.1">
+        <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>