Mercurial > repos > iuc > snpsift
diff snpSift_vcfCheck.xml @ 3:20c7d583fec1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
| author | iuc |
|---|---|
| date | Mon, 12 Jun 2017 10:25:32 -0400 |
| parents | bf8c1526871b |
| children | 09d6806c609e |
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--- a/snpSift_vcfCheck.xml Mon Dec 05 12:11:18 2016 -0500 +++ b/snpSift_vcfCheck.xml Mon Jun 12 10:25:32 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1"> +<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> @@ -7,18 +7,18 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - @CONDA_SNPSIFT_JAR_PATH@ && - java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" -]]> - </command> +SnpSift -Xmx2G vcfCheck +'$input' +> '$output' + ]]></command> <inputs> - <param format="vcf" name="input" type="data" label="Variant input file in VCF format to check"/> + <param name="input" type="data" format="vcf" label="Variant input file in VCF format to check"/> </inputs> <outputs> - <data format="vcf" name="output" /> + <data name="output" format="vcf" /> </outputs> <tests> - <test> + <test expect_exit_code="0"> <param name="input" ftype="vcf" value="test_bad.vcf"/> <assert_stderr> <has_text text="Errors" /> @@ -31,8 +31,7 @@ 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 -]]> - </help> +- http://snpeff.sourceforge.net/SnpSift.html#vcfCheck + ]]></help> <expand macro="citations" /> </tool>