Mercurial > repos > iuc > snpsift
diff snpSift_int.xml @ 1:98708b88af9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 10:04:09 -0400 |
| parents | 9e8280e19338 |
| children | bf8c1526871b |
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--- a/snpSift_int.xml Thu Jan 22 08:39:07 2015 -0500 +++ b/snpSift_int.xml Tue Jun 07 10:04:09 2016 -0400 @@ -1,14 +1,17 @@ -<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) --> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> - <command> - java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output" +]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> @@ -19,7 +22,6 @@ <outputs> <data format="vcf" name="output" /> </outputs> - <expand macro="stdio" /> <tests> <test> <param name="input" ftype="vcf" value="annotate_5.vcf"/> @@ -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>