view rmarkdown_report.xml @ 0:389ef73cf4e1 draft

planemo upload

<tool id="find_ssrs" name="aurora_find_ssrs" version="1.0.0">
  <description>Identifies simple sequence repeats (SSRs) and calls primers from the sequences in a fastq formatted file.&#xD;
    </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="1.6">r-rmarkdown</requirement><requirement type="package" version="2.50">perl-getopt-long</requirement><requirement type="package" version="1.7.2">perl-bioperl</requirement><requirement type="package" version="0.98">perl-excel-writer-xlsx</requirement><requirement type="package" version="2.4.1a">primer3</requirement></requirements>
  <command><![CDATA[        ######### each aurora tool generates a html file and have an files path directory associated with it.
        mkdir -p $report.files_path &&

        ######### three important paths:
        #########   1. path to tool installation directory
        #########   2. path to report html
        #########   3. path to files_path directory associated with the report output.
        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
        export REPORT='$report' &&
        export REPORT_FILES_PATH='$report.files_path' &&

        ############ create a hidden file to store r markdown rendering log
        touch $report.files_path/r_rendering.log.txt &&

        ############ finally run the render.R script
        Rscript '${__tool_directory__}/rmarkdown_report_render.R'

            -o $report
            -d $report.files_path

            -f $fasta_file
            -m $masked_file

            -F $ssr_fasta
            -S $ssr_stats
            -R $ssr_report


]]></command>
  <inputs>
    <param type="data" name="fasta_file" argument="-f" label="Fasta file" help="The file of the sequences to be searched" optional="False" format="fasta,fa"/><param type="data" name="masked_file" argument="-m" label="Masked fasta file" help="A soft-masked version of the fasta file (soft masked means low complexity sequences are in lower case bases.)" optional="False" format="fasta,fa"/></inputs>
  <outputs>
        <data format="html" name="report" label="${tool.name} report on ${on_string}"/><data name="ssr_fasta" format="fasta,fa" label="${tool.name} on ${on_string} (SSR fasta)" hidden="false"/><data name="ssr_stats" format="txt" label="${tool.name} on ${on_string} (SSR stats)" hidden="false"/><data name="ssr_report" format="txt" label="${tool.name} on ${on_string} (SSR report)" hidden="false"/></outputs>
  <citations>
        <citation type="bibtex"><![CDATA[
            @article{allaire2016rmarkdown,
            title={rmarkdown: Dynamic Documents for R, 2016},
            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
            journal={R package version 0.9},
            volume={6},
            year={2016}
            }
        ]]></citation><citation type="bibtex"><![CDATA[
            @book{xie2015dynamic,
            title={Dynamic Documents with R and knitr},
            author={Xie, Yihui},
            volume={29},
            year={2015},
            publisher={CRC Press}
            }
        ]]></citation><citation type="bibtex"><![CDATA[
            @online{jstree,
            author={Bozhanov, Ivan},
            year = 2018,
            url = {https://www.jstree.com/}
            }
        ]]></citation></citations>
</tool>