# HG changeset patch
# User iuc
# Date 1480957569 18000
# Node ID 847db7b39bdcecfae65456666eef5ee848cc28b5
# Parent  9ba6e2c298ab9f2f1cab35736b3c0ce69dd3ed28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

diff -r 9ba6e2c298ab -r 847db7b39bdc snpSift_geneSets.xml
--- a/snpSift_geneSets.xml	Mon Sep 19 14:43:55 2016 -0400
+++ b/snpSift_geneSets.xml	Mon Dec 05 12:06:09 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1">
     <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)
@@ -10,8 +10,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPEFF_JAR_PATH@ &&
-        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx2G -jar "\$SNPSIFT_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"
@@ -55,14 +55,7 @@
 
 @EXTERNAL_DOCUMENTATION@
 
-@CITATION_SECTION@
-
-For `MSigDB`_, please cite |Subramanian2005|_.
-
 .. _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">
diff -r 9ba6e2c298ab -r 847db7b39bdc snpSift_macros.xml
--- a/snpSift_macros.xml	Mon Sep 19 14:43:55 2016 -0400
+++ b/snpSift_macros.xml	Mon Dec 05 12:06:09 2016 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.1">snpsift</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,12 +10,11 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
-  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
+  <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
   <xml name="version_command">
     <version_command><![CDATA[
-    if [ -z "$SNPEFF_JAR_PATH" ]; then
-        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
-    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+    if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
+    java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
     ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
@@ -25,16 +24,6 @@
 	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
-  <token name="@CITATION_SECTION@">------
-
-**Citation**
-
-For the underlying tool, please cite the following two publications:
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
-
-  </token>
   <xml name="citations">
       <citations>
         <citation type="doi">10.3389/fgene.2012.00035</citation>
diff -r 9ba6e2c298ab -r 847db7b39bdc tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Sep 19 14:43:55 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <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>