Mercurial > repos > iuc > snpsift
diff snpSift_rmInfo.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_rmInfo.xml Tue Jun 07 10:04:09 2016 -0400 +++ b/snpSift_rmInfo.xml Mon Dec 05 12:11:18 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.1"> <description>remove INFO field annotations</description> <macros> <import>snpSift_macros.xml</import> @@ -7,7 +7,10 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" rmInfo "$input" ' '.join($info_fields.split(',')) > "$output" + @CONDA_SNPSIFT_JAR_PATH@ && + java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" rmInfo "$input" + #echo ' '.join($info_fields.split(',')) + > "$output" ]]> </command> <inputs> @@ -22,7 +25,7 @@ </outputs> <tests> <test> - <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> + <param name="input" ftype="vcf" value="test_rmInfo.vcf"/> <param name="info_fields" value="EFF"/> <output name="output"> <assert_contents> @@ -31,15 +34,6 @@ </assert_contents> </output> </test> - <test> - <param name="input" ftype="vcf" value="test-data/test_rmInfo.vcf"/> - <param name="info_fields" value="EFF"/> - <output name="output"> - <assert_contents> - <not_has_text text="DP=29;EFF=EXON" /> - </assert_contents> - </output> - </test> </tests> <help><![CDATA[ This command removes INFO fields from a VCF file (i.e. removes annotations)