Mercurial > repos > iuc > snpsift
diff snpSift_int.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_int.xml Mon Dec 05 12:11:18 2016 -0500 +++ b/snpSift_int.xml Mon Jun 12 10:25:32 2017 -0400 @@ -1,6 +1,6 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1"> +<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0"> <description>Filter variants using intervals</description> - <!-- + <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <macros> @@ -10,18 +10,20 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - @CONDA_SNPSIFT_JAR_PATH@ && - java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output" -]]> - </command> +SnpSift -Xmx2G intervals +-i '$input' +$exclude +'$bedFile' +> '$output' + ]]></command> <inputs> - <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> - <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> - <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" + <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> + <param name="bedFile" type="data" format="bed" label="Intervals (BED file)"/> + <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" help="Filter out (exclude) VCF entries that match any interval in the BED files"/> </inputs> <outputs> - <data format="vcf" name="output" /> + <data name="output" format="vcf" /> </outputs> <tests> <test> @@ -48,13 +50,10 @@ </test> </tests> <help><![CDATA[ - You can filter using intervals (BED file). @EXTERNAL_DOCUMENTATION@ - http://snpeff.sourceforge.net/SnpSift.html#intervals - -]]> - </help> +- http://snpeff.sourceforge.net/SnpSift.html#intervals + ]]></help> <expand macro="citations" /> </tool>