Mercurial > repos > iuc > snpsift_genesets
changeset 1:0af41de4eda1 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 10:05:20 -0400 |
| parents | 9e6fa49c1077 |
| children | 9ba6e2c298ab |
| files | snpSift_geneSets.xml snpSift_macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 18 insertions(+), 11 deletions(-) [+] |
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--- a/snpSift_geneSets.xml Thu Jan 22 08:58:01 2015 -0500 +++ b/snpSift_geneSets.xml Tue Jun 07 10:05:20 2016 -0400 @@ -1,21 +1,23 @@ -<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="4.0.0"> +<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) --> - <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> - <command> - java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar geneSets -v + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + java -Xmx2G -jar "\$SNPEFF_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 > $output + "$input" 2> "$log" > "$output" +]]> </command> <inputs> <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> @@ -39,10 +41,9 @@ <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> </outputs> - <expand macro="stdio" /> <tests> </tests> - <help> + <help><![CDATA[ This tool uses `SnpSift GeneSets`_ to add annotations from `MSigDB`_, a collection of annotated gene sets from different sources including Gene Ontology (GO), KEGG, Reactome. .. _SnpSift GeneSets: http://snpeff.sourceforge.net/SnpSift.html#geneSets @@ -60,6 +61,8 @@ .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ .. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550 .. _Subramanian2005: http://www.pnas.org/content/102/43/15545 + +]]> </help> <expand macro="citations"> <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
--- a/snpSift_macros.xml Thu Jan 22 08:58:01 2015 -0500 +++ b/snpSift_macros.xml Tue Jun 07 10:05:20 2016 -0400 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.0">snpEff</requirement> + <requirement type="package" version="4.1">snpEff</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,6 +10,10 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> + <xml name="version_command"> + <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command> + </xml> + <token name="@WRAPPER_VERSION@">4.1</token> <token name="@EXTERNAL_DOCUMENTATION@"> For details about this tool, please go to:
--- a/tool_dependencies.xml Thu Jan 22 08:58:01 2015 -0500 +++ b/tool_dependencies.xml Tue Jun 07 10:05:20 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="snpEff" version="4.0"> - <repository changeset_revision="6bc55957927b" name="package_snpeff_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="snpEff" version="4.1"> + <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>