Mercurial > repos > iuc > snpsift
diff snpSift_vcfCheck.xml @ 13:ed810da439cc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 09:41:13 -0400 |
| parents | b884686a80dc |
| children | 80da7fae14b8 |
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--- a/snpSift_vcfCheck.xml Tue Oct 13 17:31:24 2015 -0400 +++ b/snpSift_vcfCheck.xml Tue Jun 07 09:41:13 2016 -0400 @@ -1,12 +1,14 @@ -<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="4.0.0"> +<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0"> <description>basic checks for Vcf specification compliance</description> <macros> <import>snpSift_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> - <command> - java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar vcfCheck $input > $output + <expand macro="version_command" /> + <command><![CDATA[ + java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" +]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> @@ -24,16 +26,16 @@ </output> </test> </tests> - <help> + <help><![CDATA[ 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 -@CITATION_SECTION@ - +]]> </help> + <expand macro="citations" /> </tool>