annotate tool_dependencies.xml @ 8:0753bd9cb8a1 draft

planemo upload for repository https://github.com/nitesh1989/tools-iuc/tree/methylation/tool_collections/methylation_toolkit/minfi commit cd2aa0df28d6d740d86c5aec560f51e74ef3510d-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="libcurl" version="7.35">
        <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <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="r-getopt" version="1.20.0">
        <repository changeset_revision="712cb82311a8" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="minfi" version="1.16.0">
        <install version="1.0">
        <actions>
            <action type="setup_r_environment">
                <repository changeset_revision="0d934b13250c" name="package_libcurl_7_35" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                    <package name="libcurl" version="7.35" />
                </repository>
                <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>
                <package>https://bioarchive.galaxyproject.org/BiocGenerics_0.16.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/Biobase_2.29.1.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/S4Vectors_0.8.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/IRanges_2.4.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/GenomeInfoDb_1.6.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/zlibbioc_1.16.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/XVector_0.10.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/GenomicRanges_1.22.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/Biostrings_2.38.0.tar.gz</package>
<!--            <package>https://bioarchive.galaxyproject.org/iterators_1.0.8.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/foreach_1.4.3.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/locfit_1.5-9.1.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/matrixStats_0.14.2.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/limma_3.26.0.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/registry_0.3.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/digest_0.6.8.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/stringi_0.5-5.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/magrittr_1.5.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/stringr_1.0.0.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/xtable_1.7-4.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/pkgmaker_0.22.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/rngtools_1.2.4.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/doRNG_1.6.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/DBI_0.3.1.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/RSQLite_1.0.0.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/AnnotationDbi_1.31.17.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/bitops_1.0-6.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/RCurl_1.95-4.7.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/XML_3.98-1.3.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/lambda.r_1.1.7.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/futile.options_1.0.0.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/futile.logger_1.4.1.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/snow_0.3-13.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/BiocParallel_1.3.54.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/Rsamtools_1.22.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/GenomicAlignments_1.6.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/rtracklayer_1.30.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/biomaRt_2.25.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/GenomicFeatures_1.22.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/bumphunter_1.10.0.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/beanplot_1.2.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/RColorBrewer_1.1-2.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/nor1mix_1.2-1.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/multtest_2.26.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/siggenes_1.44.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/preprocessCore_1.32.0.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/base64_1.1.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/illuminaio_0.12.0.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/mclust_5.0.2.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/annotate_1.48.0.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/genefilter_1.52.0.tar.gz</package>
                <!-- <package>https://bioarchive.galaxyproject.org/Rcpp_0.12.1.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/plyr_1.8.3.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/reshape_0.8.5.tar.gz</package> -->
                <!-- <package>https://bioarchive.galaxyproject.org/quadprog_1.5-5.tar.gz</package> -->
                <package>https://bioarchive.galaxyproject.org/GEOquery_2.35.7.tar.gz</package>
                <package>https://bioarchive.galaxyproject.org/minfi_1.16.0.tar.gz</package>
            </action>
        </actions>
        </install>
    <readme>
    </readme>
</package>
</tool_dependency>