# HG changeset patch
# User iuc
# Date 1430793430 14400
# Node ID fc8a3e1e788093de05d01e517aff40882aaf28d4
# Parent  f915cd331e538bccc0cb6bac672cbce1516c2fd5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 344140b8df53b8b7024618bb04594607a045c03a

diff -r f915cd331e53 -r fc8a3e1e7880 snpSift_dbnsfp.xml
--- a/snpSift_dbnsfp.xml	Sun May 03 22:47:36 2015 -0400
+++ b/snpSift_dbnsfp.xml	Mon May 04 22:37:10 2015 -0400
@@ -1,13 +1,14 @@
 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="4.0.0">
     <description>Add Annotations from dbNSFP</description>
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
         java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
         #if $db.dbsrc == 'cached' :
-          -db $db.dbnsfp 
+          -db $db.dbnsfp
           #if $db.annotations and $db.annotations.__str__ != '':
             -f "$db.annotations"
           #end if
@@ -16,8 +17,8 @@
           #if $db.annotations and $db.annotations.__str__ != '':
             -f "$db.annotations"
           #end if
-        #end if          
-        $input > $output  
+        #end if
+        $input > $output
         2> tmp.err &amp;&amp; grep -v file tmp.err
     </command>
     <inputs>
@@ -53,7 +54,6 @@
             </when>
         </conditional>
     </inputs>
-    <expand macro="stdio" />
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
@@ -241,13 +241,13 @@
     rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
 
 
-The website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 genome builds. 
+The website for  dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP  and there is only annotation for human hg18 and hg19 genome builds.
 
 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
 
-	- The first line of the file must be column headers that name the annotations.  
+	- The first line of the file must be column headers that name the annotations.
 	- The first 4 columns are required and must be::
-		1. chromosome 
+		1. chromosome
 		2. position in chromosome
 		3. reference base
 		4. alternate base
diff -r f915cd331e53 -r fc8a3e1e7880 snpSift_geneSets.xml
--- a/snpSift_geneSets.xml	Sun May 03 22:47:36 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 f915cd331e53 -r fc8a3e1e7880 tool-data/snpeff_msigdb_database.loc.sample
--- a/tool-data/snpeff_msigdb_database.loc.sample	Sun May 03 22:47:36 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