<tool id="polca" name="polca" version="@VERSION@">
    <description> Improving the consensus accuracy in genome assemblies</description>
    <macros>
        <token name="@VERSION@">4.0.9</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">masurca</requirement>
    </requirements>
    <version_command>polca --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        #if $short_reads.sr_type == 'paired'
            ln -s '$short_read.R1' reads_1.fastq.gz &&
            ln -s '$short_read.R2' reads_2.fastq.gz &&
        #else if str($short_reads.sr_type) == "collection"
            ln -s '$short_read.input1.forward' reads_1.fastq.gz &&
            ln -s '$short_read.input1.reverse' reads_2.fastq.gz &&
        #end if
        ln -s '${contigs}' contigs.fa &&
        polca.sh -a contigs.fa
        -r reads1.fastq.gz reads2.fastq.gz
        -t \${GALAXY_SLOTS:-4}
        -m 1G
    ]]>    </command>

    <inputs>
        <param name="contigs" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Long-read assembly"/>
        <conditional name="short_reads">
            <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
                <option value="paired" selected="true">Paired End</option>
                <option value="collection">Paired Collection</option>
            </param>
            <when value="paired">
                <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
                <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
            </when>
            <when value="collection">
                <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="contigs" format="fasta" from_work_dir="contigs.PolcaCorrected.fa" label="${tool.name} on ${on_string} Polished assembly" />
        <data name="report" format="txt" from_work_dir="contigs.report" label="${tool.name} on ${on_string} Polished report" />
    </outputs>
    <help><![CDATA[
    ]]>    </help>
</tool>