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<tool id="statonlab_hmmscan" name="aurora_statonlab_hmmscan" version="1.0.0">
    <description>Query protein sequences against Pfam database&#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="3.2.1">hmmer</requirement>
        <requirement type="package" version="1.6">r-rmarkdown</requirement>
        <requirement type="package" version="0.8.1">seqkit</requirement>
        <requirement type="package" version="1.1.1">r-tidyverse</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
            -g $significant_genes
            -u $protein_sequences_url

            -E $evalue_threshold
            -T $score_threshold
            -e $domE
            -t $domT
            -b $best_hit
            -1 $pfam_tbl_out
]]></command>
    <inputs>
        <param type="data" name="significant_genes" label="Significant Genes"
               help="A significant genes file from the &lt;code&gt;aurora_deseq2&lt;/code&gt; tool." optional="False"
               format="txt,csv" multiple="False"/>
        <param type="text" name="protein_sequences_url" label="URL to a protein sequences file" optional="False"/>
        <param type="text" name="evalue_threshold" argument="-E" label="Evalue threshold" optional="True"
               help="report models &lt;= this E-value threshold in output  [10.0]  (x&gt;0)" optional="False"
               value="10"/>
        <param type="text" name="score_threshold" argument="-T" label="Score threshold" optional="True"
               help="report models &gt;= this score threshold in output" optional="False"/>
        <param type="text" name="domE" argument="--domE" label="domains E-value threshold" optional="True"
               help="report domains &lt;= this E-value threshold in output  [10.0]  (x&gt;0)" optional="False"
               value="10"/>
        <param type="text" name="domT" argument="--domT" label="domains score threshold" optional="True"
               help="report domains &gt;= this score cutoff in output" optional="False"/>
        <param type="boolean" name="best_hit" label="Best Hit" help="Only return best hit for each query sequence"
               optional="False" truevalue="NO_ARGUMENT_YES" falsevalue="NO_ARGUMENT_NO"/>
    </inputs>
    <outputs>
        <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
        <data name="pfam_tbl_out" format="csv" label="${tool.name} pfam.domtblout on ${on_string}" 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>
        <citation type="bibtex"><![CDATA[@article{eddy1992hmmer,
  title={HMMER user’s guide},
  author={Eddy, Sean},
  journal={Department of Genetics, Washington University School of Medicine},
  volume={2},
  number={1},
  year={1992}
}]]></citation>
    </citations>
</tool>