Mercurial > repos > iuc > snpsift
diff snpSift_vartype.xml @ 15:8bd645802765 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 10:24:36 -0400 |
| parents | 80da7fae14b8 |
| children | ede8954f5c82 |
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--- a/snpSift_vartype.xml Mon Dec 05 12:10:54 2016 -0500 +++ b/snpSift_vartype.xml Mon Jun 12 10:24:36 2017 -0400 @@ -7,16 +7,17 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - @CONDA_SNPSIFT_JAR_PATH@ && - java -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output" -]]> - </command> +SnpSift varType +'$input' +2> '$log' +> '$output' + ]]></command> <inputs> - <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> + <param name="input" type="data" format="vcf" label="Variant file (VCF)"/> </inputs> <outputs> - <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> - <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> + <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" /> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log" /> </outputs> <tests> </tests> @@ -35,7 +36,6 @@ .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: https://opensource.org/licenses/MIT -]]> - </help> + ]]></help> <expand macro="citations" /> </tool>