Mercurial > repos > iuc > snpsift_genesets
diff snpSift_geneSets.xml @ 5:d12a810c837e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
| author | iuc |
|---|---|
| date | Mon, 12 Jun 2017 10:25:57 -0400 |
| parents | 847db7b39bdc |
| children |
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--- a/snpSift_geneSets.xml Mon Dec 19 11:57:27 2016 -0500 +++ b/snpSift_geneSets.xml Mon Jun 12 10:25:57 2017 -0400 @@ -1,6 +1,6 @@ -<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1"> +<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0"> <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description> - <!-- + <!-- You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) --> <macros> @@ -10,22 +10,22 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - @CONDA_SNPSIFT_JAR_PATH@ && - java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" geneSets -v - #if $db_opts.db_opts_selector == "db" - "${db_opts.database.fields.path}" - #elif $db_opts.db_opts_selector == "histdb" - "$db_opts.histdb" - #end if - "$input" 2> "$log" > "$output" -]]> - </command> +SnpSift -Xmx2G geneSets -v +#if $db_opts.db_opts_selector == 'db' + '${db_opts.database.fields.path}' +#elif $db_opts.db_opts_selector == 'histdb' + '$db_opts.histdb' +#end if +'$input' +2> '$log' +> '$output' + ]]></command> <inputs> - <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> + <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> <conditional name="db_opts"> <param name="db_opts_selector" type="select" label="Select Annotation database" help=""> - <option value="db" selected="True">Locally installed database</option> - <option value="histdb">database from your history</option> + <option value="db" selected="True">Locally installed database</option> + <option value="histdb">database from your history</option> </param> <when value="db"> <param name="database" type="select" label="Molecular Signatures Database (MSigDB)"> @@ -39,8 +39,8 @@ </conditional> </inputs> <outputs> - <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> - <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> + <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" /> + <data name="log" format="txt" label="${tool.name} on ${on_string}: log" /> </outputs> <tests> </tests> @@ -56,8 +56,7 @@ @EXTERNAL_DOCUMENTATION@ .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ -]]> - </help> + ]]></help> <expand macro="citations"> <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation --> </expand>