Mercurial > repos > iuc > snpsift

diff snpSift_int.xml @ 11:b884686a80dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:06 -0400
parents f0faaa4d6ee5
children ed810da439cc
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line diff
--- a/snpSift_int.xml	Wed Apr 29 11:55:50 2015 -0400
+++ b/snpSift_int.xml	Mon May 04 22:37:06 2015 -0400
@@ -1,25 +1,25 @@
 <tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
     <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)
     -->
-    <expand macro="requirements" />
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command>
         java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar 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="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" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="annotate_5.vcf"/>