view fastq_dump_se.xml @ 9:233210d44681 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_fastq_dump commit 5d2a63708a8abf73432c1d6863d970146c6a38b2-dirty

<tool id="rmarkdown_fastqc_dump_se" name="fastqc-dump-se" 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>
    </requirements>
    <description>
        Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
        collection.
    </description>
    <stdio>
        <regex match="Execution halted"
               source="both"
               level="fatal"
               description="Execution halted." />
        <regex match="Error in"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
        <regex match="Fatal error"
               source="both"
               level="fatal"
               description="An undefined error occured, please check your intput carefully and contact your administrator." />
    </stdio>
    <command>
        <![CDATA[
            Rscript '${__tool_directory__}/fastq_dump_se_render.R'
                -i '$sra_accession'
                -e $echo
                -f $format

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

                -t '${__tool_directory__}/fastq_dump_se.Rmd'
        ]]>
    </command>
    <inputs>
        <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
               help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
        <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (Yes) or fasta (No)?"/>
        <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="Fastq-dump (single end reads)" />
        <collection type="list" name="list_collection">
            <discover_datasets pattern="__name_and_ext__" directory="read_files_directory" />
        </collection>
        <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" />
    </outputs>
</tool>