view bdss_client_sra.xml @ 0:1cc0ed4567e1 draft default tip

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client_main commit d9ab791a7ce12362dc6e28c0a518a3f23dd581fe-dirty

<tool id="rmarkdown_bdss_client_sra" name="BDSS client SRA" version="1.0.3">
    <requirements>
        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
        <requirement type="package" version="3.3.2">r-base</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 and generate list (single end SRA data) and list:paired dataset collection
        (paired end SRA data).
    </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 '${__tool_directory__}/bdss_client_sra_render.R'
                -i '$sra_ids_se'
                -p '$sra_ids_pe'
                -f $format
                -e $echo

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

                -t '${__tool_directory__}/bdss_client_sra.Rmd'
        ]]>
    </command>
    <inputs>
        <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA"
               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/>
        <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA"
               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1748507"/>
        <param type="select" name="format" label="Output format">
            <option value="fastq" selected="true">fastq</option>
            <option value="fasta">fasta</option>
        </param>
        <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 client report"/>
        <!--list dataset collection for single end SRA data-->
        <collection type="list" name="list_collection" label="BDSS download data (single end reads)">
            <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/>
        </collection>
        <!--list:paired dataset collection for paired end SRA data-->
        <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)">
            <discover_datasets
                    pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?"
                    directory="pe_read_files_directory"/>
        </collection>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
    </outputs>
</tool>