view tool_dependencies.xml @ 1:24d23efd6255 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_r_3_2_1_goseq_1_22_0 commit 808b173b79976002d864d88077837871f88c5f2c

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.2.1">
        <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="libxml2" version="2.9.1">
        <repository changeset_revision="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="goseq" version="1.22.0">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="R" version="3.2.1" />
                    </repository>
                    <!-- libxml2 needs to be sourced after R because R also was compiled against a different version of libxml2 -->
                    <repository changeset_revision="45b16a3ab504" name="package_libxml2_2_9_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="libxml2" version="2.9.1" />
                    </repository>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/BiasedUrn_1.07.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/BiocGenerics_0.16.1.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/S4Vectors_0.8.11.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/IRanges_2.4.7.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/GenomeInfoDb_1.6.3.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/zlibbioc_1.16.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/XVector_0.10.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/GenomicRanges_1.22.4.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/XML_3.98-1.3.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/Biostrings_2.38.4.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/bitops_1.0-6.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/RCurl_1.95-4.7.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/lambda.r_1.1.7.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/futile.options_1.0.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/futile.logger_1.4.1.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/snow_0.4-1.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/BiocParallel_1.4.3.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/Rsamtools_1.22.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/Biobase_2.30.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/GenomicAlignments_1.6.3.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/rtracklayer_1.30.2.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/DBI_0.3.1.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/RSQLite_1.0.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/AnnotationDbi_1.32.3.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/biomaRt_2.26.1.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/GenomicFeatures_1.22.13.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/geneLenDataBase_1.6.0.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/GO.db_3.2.2.tar.gz?raw=true</package>
                        <package>https://github.com/mvdbeek/galaxy_tool_source/blob/master/3_2_1/goseq_1.22.0.tar.gz?raw=true</package>
                </action>
            </actions>
        </install>
        <readme>
            goseq Gene Ontology analyser
            -----
            Does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data.
            By default, tests gene ontology (GO) categories, but any categories may be tested.
        </readme>
    </package>
</tool_dependency>