Mercurial > repos > iuc > snpsift_genesets
changeset 3:847db7b39bdc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
| author | iuc |
|---|---|
| date | Mon, 05 Dec 2016 12:06:09 -0500 |
| parents | 9ba6e2c298ab |
| children | ea2e7d299365 |
| files | snpSift_geneSets.xml snpSift_macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 7 insertions(+), 31 deletions(-) [+] |
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--- a/snpSift_geneSets.xml Mon Sep 19 14:43:55 2016 -0400 +++ b/snpSift_geneSets.xml Mon Dec 05 12:06:09 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0"> +<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1"> <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) @@ -10,8 +10,8 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - @CONDA_SNPEFF_JAR_PATH@ && - java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v + @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 $db_opts.db_opts_selector == "histdb" @@ -55,14 +55,7 @@ @EXTERNAL_DOCUMENTATION@ -@CITATION_SECTION@ - -For `MSigDB`_, please cite |Subramanian2005|_. - .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/ -.. |Subramanian2005| replace:: Subramanian, A., *et al.* (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. *Proc. Natl. Acad. Sci. U.S.A.* 102(43), 15545-15550 -.. _Subramanian2005: http://www.pnas.org/content/102/43/15545 - ]]> </help> <expand macro="citations">
--- a/snpSift_macros.xml Mon Sep 19 14:43:55 2016 -0400 +++ b/snpSift_macros.xml Mon Dec 05 12:06:09 2016 -0500 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.1">snpEff</requirement> + <requirement type="package" version="4.1">snpsift</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,12 +10,11 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token> + <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token> <xml name="version_command"> <version_command><![CDATA[ - if [ -z "$SNPEFF_JAR_PATH" ]; then - export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff))); - fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version + if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi && + java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1 ]]></version_command> </xml> <token name="@WRAPPER_VERSION@">4.1</token> @@ -25,16 +24,6 @@ http://snpeff.sourceforge.net/SnpEff_manual.html </token> - <token name="@CITATION_SECTION@">------ - -**Citation** - -For the underlying tool, please cite the following two publications: - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012. - - </token> <xml name="citations"> <citations> <citation type="doi">10.3389/fgene.2012.00035</citation>
--- a/tool_dependencies.xml Mon Sep 19 14:43:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <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>