Mercurial > repos > iuc > snpsift
diff snpSift_vartype.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_vartype.xml Thu Jan 22 08:39:07 2015 -0500 +++ b/snpSift_vartype.xml Tue Jun 07 10:04:09 2016 -0400 @@ -1,11 +1,14 @@ -<tool id="snpsift_vartype" name="SnpSift Variant Type" version="4.0.0"> +<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0"> <description>Annotate with variant type</description> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> - <command> - java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2> $log > $output + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + java -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" varType "$input" 2> "$log" > "$output" +]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> @@ -14,10 +17,9 @@ <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> </outputs> - <expand macro="stdio" /> <tests> </tests> - <help> + <help><![CDATA[ **What it does** This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense). @@ -34,6 +36,8 @@ .. _MIT license: http://opensource.org/licenses/MIT @CITATION_SECTION@ + +]]> </help> <expand macro="citations" /> </tool>