Mercurial > repos > iuc > snpsift
diff snpSift_int.xml @ 13:ed810da439cc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 09:41:13 -0400 |
| parents | b884686a80dc |
| children | 80da7fae14b8 |
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--- a/snpSift_int.xml Tue Oct 13 17:31:24 2015 -0400 +++ b/snpSift_int.xml Tue Jun 07 09:41:13 2016 -0400 @@ -1,6 +1,6 @@ -<tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0"> +<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> @@ -8,13 +8,15 @@ </macros> <expand macro="requirements" /> <expand macro="stdio" /> - <command> - java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output + <expand macro="version_command" /> + <command><![CDATA[ + java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$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="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> @@ -44,14 +46,14 @@ </output> </test> </tests> - <help> + <help><![CDATA[ You can filter using intervals (BED file). @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#intervals -@CITATION_SECTION@ - +]]> </help> + <expand macro="citations" /> </tool>