<tool id="rmarkdown_collection_paired" name="Collection type (paired)" 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>
    </requirements>
    <description>
        Create a paired dataset collection from files in history.
    </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__}/collection_paired_render.R'
                -L $forward_input
                -R $reverse_input
                -e $echo
                -f $format

                -r $report
                -d $report.files_path

                -t '${__tool_directory__}/collection_paired.Rmd'
        ]]>
    </command>
    <inputs>
        <param type="data" name="forward_input" multiple="false" label="forward input"/>
        <param type="data" name="reverse_input" multiple="false" label="reverse input"/>
        <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>

        <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="Collection builder (paired collection)" />
        <collection type="paired" name="list_collection">
        </collection>
    </outputs>
</tool>