diff snpSift_filter.xml @ 8:2f40467536cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

--- 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>