Mercurial > repos > iuc > snpsift
diff snpSift_vcfCheck.xml @ 2:bf8c1526871b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
| author | iuc |
|---|---|
| date | Mon, 05 Dec 2016 12:11:18 -0500 |
| parents | 98708b88af9f |
| children | 20c7d583fec1 |
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--- a/snpSift_vcfCheck.xml Tue Jun 07 10:04:09 2016 -0400 +++ b/snpSift_vcfCheck.xml Mon Dec 05 12:11:18 2016 -0500 @@ -1,5 +1,5 @@ -<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.0"> - <description>basic checks for Vcf specification compliance</description> +<tool id="snpSift_vcfCheck" name="SnpSift vcfCheck" version="@WRAPPER_VERSION@.1"> + <description>basic checks for VCF specification compliance</description> <macros> <import>snpSift_macros.xml</import> </macros> @@ -7,7 +7,8 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" + @CONDA_SNPSIFT_JAR_PATH@ && + java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" vcfCheck "$input" > "$output" ]]> </command> <inputs> @@ -18,23 +19,19 @@ </outputs> <tests> <test> - <param name="input" ftype="vcf" value="test-data/test_bad.vcf"/> - <output name="output"> - <assert_contents> - <has_text text="Errors" /> - </assert_contents> - </output> + <param name="input" ftype="vcf" value="test_bad.vcf"/> + <assert_stderr> + <has_text text="Errors" /> + </assert_stderr> </test> </tests> <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. @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#vcfCheck - ]]> </help> <expand macro="citations" />