Mercurial > repos > iuc > snpsift

diff snpSift_vcfCheck.xml @ 11:b884686a80dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
line wrap: on
line diff
--- a/snpSift_vcfCheck.xml	Wed Apr 29 11:55:50 2015 -0400
+++ b/snpSift_vcfCheck.xml	Mon May 04 22:37:06 2015 -0400
@@ -1,9 +1,10 @@
 <tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0">
     <description>basic checks for Vcf specification compliance</description>
-    <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 vcfCheck $input > $output
     </command>
@@ -13,7 +14,6 @@
     <outputs>
         <data format="vcf" name="output" />
     </outputs>
-    <expand macro="stdio" />
     <tests>
         <test>
             <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/>
@@ -28,7 +28,7 @@
 
 Perform some basic check ups on VCF files to spot common problems.
 
-SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool. 
+SnpSift vcfCheck checks for some common problems where VCF files are not following the specification. Given that many common VCF problems cause analysis tools and pipelines to behave unexpectedly, this command is intended as a simple debugging tool.
 
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#vcfCheck