diff snpSift_geneSets.xml @ 3:847db7b39bdc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

--- 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">