comparison bdss_client.xml @ 7:efb1938c3020 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty

7:efb1938c3020

<tool id="rmarkdown_bdss_client" name="BDSS client" version="1.0.0">
    <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>
        <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
        <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
    </requirements>
    <description>
        Download data with BDSS client.
    </description>
    <stdio>
        <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
        <regex match="XXX"
               source="stderr"
               level="warning"
               description="Check the warnings_and_errors.txt file for more details."/>
    </stdio>
    <command>
        <![CDATA[
            Rscript '${__tool_directory__}/bdss_client_render.R'
                -i '$urls'
                -e $echo

                -r $report
                -d $report.files_path
                -s $sink_message

                -t '${__tool_directory__}/bdss_client.Rmd'
        ]]>
    </command>
    <inputs>
        <param type="text" name="urls" label="URLs to data files" />
        <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="BDSS report"/>
        <data name="output">
            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory"/>
        </data>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
    </outputs>
</tool>