# HG changeset patch
# User iuc
# Date 1430534842 14400
# Node ID 104afefe24a81dbef418d68e71ff85578362b82a
# Parent  98a5d415d504809514fadea06c813f6c6979198c
Uploaded

diff -r 98a5d415d504 -r 104afefe24a8 snpSift_geneSets.xml
--- a/snpSift_geneSets.xml	Fri May 01 22:37:14 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,67 +0,0 @@
-<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0">
-    <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
-        #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; $output
-    </command>
-    <inputs>
-        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
-        <conditional name="db_opts">
-            <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
-              <option value="db" selected="True">Locally installed database</option>
-              <option value="histdb">database from your history</option>
-            </param>
-            <when value="db">
-                <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
-                    <options from_data_table="snpeff_msigdb_database" />
-                </param>
-                <param name="histdb" type="hidden" value="" />
-            </when>
-            <when value="histdb">
-                <param name="histdb" type="data" format="txt" label="Molecular Signatures Database (MSigDB)" />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data format="vcf" name="output" label="${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>
-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
-
-.. class:: warningmark
-
-The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.
-
-@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">
-        <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
-    </expand>
-</tool>
diff -r 98a5d415d504 -r 104afefe24a8 tool-data/snpeff_msigdb_database.loc.sample
--- a/tool-data/snpeff_msigdb_database.loc.sample	Fri May 01 22:37:14 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-## Molecular Signatures Database (MSigDB) for SnpEff.
-## You can download MSigDb from http://www.broadinstitute.org/gsea/msigdb
-#msigdb_id	msigdb_name path_to_database
-#msigdb_08_2014 MSigDB 08-2014	/data/msigdb/08_2014/msigdb.gmt