# HG changeset patch
# User jjohnson
# Date 1460217210 14400
# Node ID 2f40467536cfcde57c910b10af46953662c99ba9
# Parent  c29f29a6f26c879e4930a03f11594bea02dd95de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

diff -r c29f29a6f26c -r 2f40467536cf snpSift_annotate.xml
--- a/snpSift_annotate.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_annotate.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,13 +10,13 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
         #if $annotate.id :
           -id
-        #elif $annotate.info_ids.__str__.strip() != '' :
+        #elif str($annotate.info_ids).strip() != '' :
           -info "$annotate.info_ids"
         #end if          
-        -q $dbSnp $input > $output 
+        -q "$dbSnp" "$input" > "$output" 
 ]]>
     </command>
     <inputs>
@@ -94,10 +94,8 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#annotate
 
-@CITATION_SECTION@
-
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
 
diff -r c29f29a6f26c -r 2f40467536cf snpSift_caseControl.xml
--- a/snpSift_caseControl.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_caseControl.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,16 +10,16 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-    java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 
-    #if $name.__str__.strip() != '':
-      -name $name
+    java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 
+    #if str($name).strip() != '':
+      -name "$name"
     #end if
     #if $ctrl.ctrl_src == 'caseString':
       '$ctrl.caseControlStr' 
     #else
       -tfam "$ctrl.tfam"
     #end if
-    $input > $output
+    "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -118,8 +118,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#casecontrol
 
-@CITATION_SECTION@
-
 ]]>
-  </help>
+    </help>
+    <expand macro="citations" />
 </tool>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_extractFields.xml
--- a/snpSift_extractFields.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_extractFields.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,9 +10,9 @@
     <command><![CDATA[
         cat "$input"
         #if $one_effect_per_line:
-          | \$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl
+          | "\$SNPEFF_JAR_PATH/scripts/vcfEffOnePerLine.pl"
         #end if 
-        | java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar extractFields 
+        | java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" extractFields 
         #if $separator:
           -s '$separator'  
         #end if
@@ -21,7 +21,7 @@
         #end if
         -
         #echo ' '.join(['"%s"' % x for x in $extract.split()])
-        > $output
+        > "$output"
 ]]>
     </command>
     <inputs>
@@ -214,8 +214,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#Extract
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_filter.xml
--- a/snpSift_filter.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_filter.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -1,5 +1,4 @@
 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
-    <options sanitize="False" />
     <description>Filter variants using arbitrary expressions</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -7,25 +6,31 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
+
     <command><![CDATA[
-        java -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse 
+        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse 
         #if $filtering.mode == 'field':
             #if $filtering.replace.pass:
                 --pass
-                #if $filtering.replace.filterId and len($filtering.replace.filterId.__str__.strip()) > 0:
+                #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
                     --filterId "$filtering.replace.filterId"
                 #end if
             #end if
-            #if $filtering.addFilter and len($filtering.addFilter.__str__.strip()) > 0:
+            #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
                 --addFilter "$filtering.addFilter"
             #end if
-            #if $filtering.rmFilter and len($filtering.rmFilter.__str__.strip()) > 0:
+            #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
                 --rmFilter "$filtering.rmFilter"
             #end if
         #end if
-         > $output
+         > "$output"
 ]]>
     </command>
+    <configfiles>
+        <configfile name="exprFile">
+$expr#slurp
+        </configfile> 
+    </configfiles>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
         <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." />
@@ -51,11 +56,6 @@
             </when>
         </conditional>
     </inputs>
-    <configfiles>
-        <configfile name="exprFile">
-$expr#slurp
-        </configfile> 
-    </configfiles>
 
     <outputs>
         <data format="vcf" name="output" />
@@ -87,7 +87,7 @@
 
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
-        <param name="expr" value="(POS >= 20175) &amp; (POS &lt; 35549)"/>
+        <param name="expr" value="(POS &gt;= 20175) &amp; (POS &lt;= 35549)"/>
         <param name="mode" value="entries"/>
         <output name="output">
             <assert_contents>
@@ -102,7 +102,7 @@
 
         <test>
         <param name="input" ftype="vcf" value="test01.vcf"/>
-        <param name="expr" value="( DP >= 5 )"/>
+        <param name="expr" value="( DP &gt;= 5 )"/>
         <param name="mode" value="entries"/>
         <output name="output">
             <assert_contents>
@@ -187,8 +187,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#filter
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_int.xml
--- a/snpSift_int.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_int.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -10,7 +10,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
+        java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
 ]]>
     </command>
     <inputs>
@@ -53,8 +53,7 @@
 @EXTERNAL_DOCUMENTATION@
     http://snpeff.sourceforge.net/SnpSift.html#intervals
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_macros.xml
--- a/snpSift_macros.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_macros.xml	Sat Apr 09 11:53:30 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 c29f29a6f26c -r 2f40467536cf snpSift_rmInfo.xml
--- a/snpSift_rmInfo.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_rmInfo.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output
+      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" rmInfo "$input" ' '.join($info_fields.split(',')) > "$output"
 ]]>
     </command>
     <inputs>
@@ -52,8 +52,7 @@
 @EXTERNAL_DOCUMENTATION@
     http://snpeff.sourceforge.net/SnpSift.html#rmInfo
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_vartype.xml
--- a/snpSift_vartype.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_vartype.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2> $log > $output
+        java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output"
 ]]>
     </command>
     <inputs>
diff -r c29f29a6f26c -r 2f40467536cf snpSift_vcfCheck.xml
--- a/snpSift_vcfCheck.xml	Mon Jan 25 17:02:52 2016 -0600
+++ b/snpSift_vcfCheck.xml	Sat Apr 09 11:53:30 2016 -0400
@@ -7,7 +7,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output
+      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output"
 ]]>
     </command>
     <inputs>
@@ -35,8 +35,7 @@
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck
 
-@CITATION_SECTION@
-
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>