diff snpSift_int.xml @ 3:20c7d583fec1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5

--- a/snpSift_int.xml	Mon Dec 05 12:11:18 2016 -0500
+++ b/snpSift_int.xml	Mon Jun 12 10:25:32 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1">
+<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
     <description>Filter variants using intervals</description>
-    <!-- 
+    <!--
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
     <macros>
@@ -10,18 +10,20 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPSIFT_JAR_PATH@ &&
-        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
-]]>
-    </command>
+SnpSift -Xmx2G intervals
+-i '$input'
+$exclude
+'$bedFile'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
-        <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
-        <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 
+        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
+        <param name="bedFile" type="data" format="bed" label="Intervals (BED file)"/>
+        <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
             help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
     </inputs>
     <outputs>
-        <data format="vcf" name="output" />
+        <data name="output" format="vcf" />
     </outputs>
     <tests>
         <test>
@@ -48,13 +50,10 @@
         </test>
     </tests>
     <help><![CDATA[
-
 You can filter using intervals (BED file).
 
 @EXTERNAL_DOCUMENTATION@
-    http://snpeff.sourceforge.net/SnpSift.html#intervals
-
-]]>
-    </help>
+- http://snpeff.sourceforge.net/SnpSift.html#intervals
+    ]]></help>
     <expand macro="citations" />
 </tool>