Mercurial > repos > iuc > snpsift
diff snpSift_annotate.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_annotate.xml Thu Jan 22 08:39:07 2015 -0500 +++ b/snpSift_annotate.xml Tue Jun 07 10:04:09 2016 -0400 @@ -1,20 +1,23 @@ -<tool id="snpSift_annotate" name="SnpSift Annotate" version="4.0.0"> +<tool id="snpSift_annotate" name="SnpSift Annotate" version="@WRAPPER_VERSION@.0"> <description>SNPs from dbSnp</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 -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd #if $annotate.id : -id - #elif $annotate.info_ids.__str__.strip() != '' : + #elif str($annotate.info_ids).strip() != '' : -info "$annotate.info_ids" #end if - -q $dbSnp $input > $output + -q "$dbSnp" "$input" > "$output" +]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> @@ -24,7 +27,7 @@ <param name="id" type="boolean" truevalue="id" falsevalue="info" checked="True" label="Only annotate ID field (do not add INFO field)" help=""/> <when value="id"/> <when value="info"> - <param name="info_ids" type="text" value="" size="60" optional="true" label="Limit INFO annotation to these INFO IDs" + <param name="info_ids" type="text" value="" optional="true" label="Limit INFO annotation to these INFO IDs" help="list is a comma separated list of fields. When blank, all INFO fields are included"> <validator type="regex" message="IDs separted by commas">^(([a-zA-Z][a-zA-Z0-9_-]*)(,[a-zA-Z][a-zA-Z0-9_-]*)*)?$</validator> </param> @@ -37,7 +40,6 @@ </help> </param> </inputs> - <expand macro="stdio" /> <outputs> <data format="vcf" name="output" /> </outputs> @@ -54,7 +56,7 @@ </output> </test> </tests> - <help> + <help><![CDATA[ This is typically used to annotate IDs from dbSnp. @@ -92,9 +94,8 @@ @EXTERNAL_DOCUMENTATION@ http://snpeff.sourceforge.net/SnpSift.html#annotate -@CITATION_SECTION@ - - +]]> </help> + <expand macro="citations" /> </tool>