comparison collection_list.xml @ 1:6be61cb4a1d5 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty

0:78018b735124

    <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>

1:6be61cb4a1d5

    <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>
        <requirement type="package" version="0.5.0">r-dplyr</requirement>
    </requirements>
    <command>
        <![CDATA[
            Rscript '${__tool_directory__}/collection_list_render.R'
                -l $file_list
                -e $echo
                -f $format

                -r $report
                -d $report.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?" />
        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="fastqc report" />
        <collection type="list" name="list_collection">
            <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
        </collection>
    </outputs>
</tool>