<tool id="confindr" name="ConFindr" version="0.1.0">
    <requirements>
        <requirement type="package" version="0.7.4">confindr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## Copy and optionally uncompress reads ##
        #if $reads.reads_select == 'collection'
            #set forward=$reads.coll.forward
            #set reverse=$reads.coll.reverse
            #set name=$reads.coll.name.replace(' ', '_')
        #else
            #set name=$forward.name.split('_')[0]
        #end if
            mkdir ./${name}
        #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
            && cp $forward ./${name}/${name}_R1.fastq.gz
        #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
            && tar -vxjOf $forward > ./${name}/${name}_R1.fastq
        #else
            && cp $forward ./${name}/${name}_R1.fastq
        #end if
        #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
            && cp $reverse ./${name}/${name}_R2.fastq.gz
        #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
            && tar -vxjOf $reverse > ./${name}/${name}_R2.fastq
        #else
            && cp $reverse ./${name}/${name}_R2.fastq
        #end if
        ## !!! confindr in single-threaded mode; race condition bugs in multiple threads !!! ##
        && confindr.py -i ./${name} -o ./output -t 1
        && cat ./output/confindr_log.txt
        && ls -lah ./output/confindr_report.csv

    ]]></command>
    <inputs>
        <conditional name="reads">
            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
                <option value="collection">Paired collection from your history</option>
                <option value="history">Two FASTQ datasets from your history</option>
            </param>
            <when value="collection">
                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
            </when>
            <when value="history">
                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="csv" name="contam_report" label="Contamination Report" from_work_dir="./output/confindr_report.csv" />
    </outputs>
    <tests>
        <test>
            <param name="reads_select" value="collection" />
            <param name="coll">
                <collection type="paired">
                    <element name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz" />
                    <element name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz" />
                </collection>
            </param>
            <output name="contam_report" value="confindr_report.csv" />
        </test>
        <test>
            <param name="reads_select" value="history" />
            <param name="forward" value="example_R1.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="reverse" value="example_R2.fastq.gz" ftype="fastqsanger.gz"/>
            <output name="contam_report" value="confindr_report_2.csv" />
        </test>
        <test>
            <param name="reads_select" value="history" />
            <param name="forward" value="example_R1.fastq.bz2" ftype="fastqsanger.bz2"/>
            <param name="reverse" value="example_R2.fastq.bz2" ftype="fastqsanger.bz2"/>
            <output name="contam_report" value="confindr_report_2.csv" />
        </test>
    </tests>
    <help><![CDATA[
        ConFindr, a contamination screen for Illumina sequencing
    ]]></help>
    <citations>
        <citation type="doi">10.7717/peerj.6995</citation>
        <citation type="bibtex">
@misc{githubConFindr,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {ConFindr},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/OLC-Bioinformatics/ConFindr},
}</citation>
    </citations>
</tool>