# HG changeset patch
# User jjohnson
# Date 1460217271 14400
# Node ID 772825adad2f1c4480193e4dd3a223771322ae4d
# Parent  b5e03b2cb81362dd40aef21a25988fffe9cf9fd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

diff -r b5e03b2cb813 -r 772825adad2f snpSift_dbnsfp.xml
--- a/snpSift_dbnsfp.xml	Wed Dec 09 14:07:32 2015 -0500
+++ b/snpSift_dbnsfp.xml	Sat Apr 09 11:54:31 2016 -0400
@@ -7,19 +7,19 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar dbnsfp -v
-        #if $db.dbsrc == 'cached' :
-          -db $db.dbnsfp 
-          #if $db.annotations and $db.annotations.__str__ != '':
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v
+        #if $db.dbsrc == 'cached':
+          -db "$db.dbnsfp"
+          #if $db.annotations and str($db.annotations) != '':
             -f "$db.annotations"
           #end if
-        #else :
+        #else:
           -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
-          #if $db.annotations and $db.annotations.__str__ != '':
+          #if $db.annotations and str($db.annotations) != '':
             -f "$db.annotations"
           #end if
-        #end if          
-        $input > $output  
+        #end if
+        "$input" > "$output"
         2> tmp.err && grep -v file tmp.err
 ]]>
     </command>
@@ -284,4 +284,12 @@
 
 ]]>
     </help>
+    <expand macro="citations">
+        <citation type="doi">DOI: 10.1002/humu.21517</citation>
+        <citation type="doi">DOI: 10.1002/humu.22376</citation>
+        <citation type="doi">DOI: 10.1002/humu.22932</citation>
+        <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
+        <citation type="doi">doi: 10.1093/nar/gku1206</citation>
+        <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
+    </expand>
 </tool>
diff -r b5e03b2cb813 -r 772825adad2f snpSift_macros.xml
--- a/snpSift_macros.xml	Wed Dec 09 14:07:32 2015 -0500
+++ b/snpSift_macros.xml	Sat Apr 09 11:54:31 2016 -0400
@@ -11,7 +11,7 @@
     </stdio>
   </xml>
   <xml name="version_command">
-    <version_command>java -jar $SNPEFF_JAR_PATH/SnpEff.jar -version</version_command>
+    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
diff -r b5e03b2cb813 -r 772825adad2f tool-data/snpsift_dbnsfp.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/snpsift_dbnsfp.loc.sample	Sat Apr 09 11:54:31 2016 -0400
@@ -0,0 +1,2 @@
+#id	desc	path	annotations
+#GRCh37_dbNSFP2.1	GRCh37 dbNSFP2.1	/depot/snpeff/	SIFT_pred,Uniprot_acc
diff -r b5e03b2cb813 -r 772825adad2f tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 09 14:07:32 2015 -0500
+++ b/tool_dependencies.xml	Sat Apr 09 11:54:31 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="snpEff" version="4.1">
-        <repository changeset_revision="02a5e07a4121" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="625bc8f7929d" name="package_snpeff_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>