<tool id="polypolish" name="polypolish" version="@VERSION@">
    <description> Polishing genome assemblies with short reads</description>
    <macros>
        <token name="@VERSION@">0.5.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">polypolish</requirement>
        <requirement type="package" version="1.15.1">samtools</requirement>
        <requirement type="package" version="0.7.17">bwa</requirement>
    </requirements>
    <version_command>polypolish --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 '${assembly}' draft.fa &&
        bwa index draft.fa &&
        bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_1.fastq.gz > alignments_1.sam &&
        bwa mem -t \${GALAXY_SLOTS:-4} -a draft.fa reads_2.fastq.gz > alignments_2.sam &&
        polypolish_insert_filter.py --in1 alignments_1.sam --in2 alignments_2.sam --out1 filtered_1.sam --out2 filtered_2.sam &&
        polypolish 
        #if $debug
            $debug debug.tsv
        #end if
        -d ${min_depth} 
        -i ${fraction_invalid} 
        -m ${max_errors} 
        -v ${fraction_valid}
        draft.fasta filtered_1.sam filtered_2.sam 
        > polished.fasta
    ]]>    </command>

    <inputs>
        <param name="basecalled" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Basecalled data"/>
        <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>
        <param argument="min_depth" type="integer" value="5" min="1" label="Minimum depth" />
        <param argument="fraction_invalid" type="float" value="0.2" min="0.0" max="1.0" label="Fraction value of the read depth to be considered invalid" />
        <param argument="fraction_valid" type="integer" value="10" min="1" label="Ignore alignments with more than this many mismatches and indels" />
        <param argument="max_errors" type="integer" value="10" min="1" label="Fraction value of the read depth to be considered invalid" />
        <param argument="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Debug output" />
    </inputs>
    <outputs>
    <data name="polished" format="fasta" from_work_dir="polished.fasta" label="${tool.name} on ${on_string} Polished assembly" />
    <data name="debug" format="tabular" from_work_dir="debug.tsv" label="${tool.name} on ${on_string} Polished assembly" >
        <filter>debug is True</filter>
    </data>
    </outputs>
    <help><![CDATA[
    ]]>    </help>
</tool>