annotate tool_dependencies.xml @ 0:4a085ebd7061 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_junctionseq_0_4_19 commit e8043fd8668d06c7e08204d337c7604938af5e4c

<?xml version="1.0"?>
<tool_dependency>
    <package name="R" version="3.2.1">
        <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="JunctionSeq" version="0.4.19">
        <install version="1.0">
            <actions>
                <action type="setup_r_environment">
                    <repository changeset_revision="e46a7803f17b" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="R" version="3.2.1" />
                    </repository>
                    <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/statmod_1.4.21.tar.gz</package>
                    <package>https://mran.revolutionanalytics.com/snapshot/2015-10-29/src/contrib/plotrix_3.6.tar.gz</package>
                    <package>https://mran.revolutionanalytics.com/snapshot/2015-10-29/src/contrib/stringi_1.0-1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/magrittr_1.5.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/stringr_1.0.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/BiocGenerics_0.17.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/locfit_1.5-9.1.tar.gz</package>
                    <package>https://mran.revolutionanalytics.com/snapshot/2015-10-29/src/contrib/Rcpp_0.12.1.tar.gz</package>
                    <package>https://mran.revolutionanalytics.com/snapshot/2015-10-29/src/contrib/RcppArmadillo_0.6.100.0.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/lambda.r_1.1.7.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/futile.options_1.0.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/futile.logger_1.4.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/snow_0.3-13.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/BiocParallel_1.5.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/S4Vectors_0.9.6.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/IRanges_2.5.5.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/RSQLite_1.0.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/AnnotationDbi_1.31.17.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/XML_3.98-1.3.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/xtable_1.7-4.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/annotate_1.49.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/genefilter_1.51.0.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/RColorBrewer_1.1-2.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/geneplotter_1.47.0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/plyr_1.8.3.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/digest_0.6.8.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/gtable_0.1.2.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/reshape2_1.4.1.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/dichromat_2.0-0.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/colorspace_1.2-6.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/munsell_0.4.2.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/labeling_0.3.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/scales_0.3.0.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/proto_0.3-10.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/ggplot2_1.0.1.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/Formula_1.2-1.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/latticeExtra_0.6-26.tar.gz</package>
                    <package>https://depot.galaxyproject.org/package/noarch/acepack_1.3-3.3.tar.gz</package>
                    <package>https://github.com/bgruening/download_store/raw/master/DESeq2-1_8_1/gridExtra_2.0.0.tar.gz</package>
                    <package>https://mran.revolutionanalytics.com/snapshot/2015-10-29/src/contrib/Hmisc_3.17-0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/zlibbioc_1.17.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/XVector_0.11.0.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.5.8.tar.gz</package>
                    <package>https://bioarchive.galaxyproject.org/GenomicRanges_1.21.15.tar.gz</package>
                    <package>https://github.com/hartleys/JunctionSeq/raw/v0.4.19/JunctionSeq_0.4.19.tar.gz</package>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>