annotate collection_list.xml @ 0:78018b735124 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty

<tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0">
    <description>
        Create a 'list' dataset collection from a set of files in Galaxy history.
    </description>
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="1.2">r-rmarkdown</requirement>
        <requirement type="package" version="0.3.5">r-htmltools</requirement>
    </requirements>
    <command>
        <![CDATA[
            Rscript '${__tool_directory__}/collection_list_render.R'
                -l $file_list
                -e $echo

                -r $report
                -o $list_collection
                -d $list_collection.files_path

                -t '${__tool_directory__}/collection_list.Rmd'
        ]]>
    </command>
    <inputs>
        <param type="data" name="file_list" multiple="true" />
        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
    </inputs>
    <outputs>
        <data format="html" name="report" label="fastqc report" />
        <collection type="list" name="list_collection">
            <discover_datasets pattern="(?P&lt;name&gt;.*)" directory="files_directory" />
        </collection>
    </outputs>
</tool>