comparison snpSift_geneSets.xml @ 3:847db7b39bdc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

2:9ba6e2c298ab

<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>

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPEFF_JAR_PATH@ &&
        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

The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.

@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">
        <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
    </expand>

3:847db7b39bdc

<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)
    -->
    <macros>

    </macros>
    <expand macro="requirements" />
    <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

The input VCF file must be annotated using SnpEff before performing GeneSets annotations. This is because the tool must know which gene the variant affects.

@EXTERNAL_DOCUMENTATION@

.. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
]]>
    </help>
    <expand macro="citations">
        <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
    </expand>