<?xml version='1.0' encoding='UTF-8'?>
<macros>
    <token name="@WRAPPER_VERSION@">0.14</token>
    <xml name="requirements_stdio">
        <requirements>
            <requirement type="package" version="0.1.19">samtools</requirement>
            <yield/>
        </requirements>
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
        <version_command>bismark --version</version_command>
    </xml>

    <xml name="single_paired_conditional">
        <!-- Input Parameters -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
            </when>
            <when value="paired">
                <repeat name="mate_list" title="Paired End Pairs" min="1">
                    <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
                    <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
                </repeat>
                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
            </when>
        </conditional>
    </xml>

    <xml name="advanced_params">
        <param name="seed_len" type="integer" value="28" label="Seed length"
            help="The number of bases of the high quality end of the read to which the maximum number of mismatches applies. (--seed-len)" />
        <param name="qupto" type="integer" value="0" min="0" label="Only aligns the first N reads or read pairs from the input"
            help="Default is 0 and means 'no-limit'. (--qupto)"/>
        <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input"
            help="(--skip-reads)" />

        <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
            label="Write ambiguous reads to an extra output file"
            help="Write all reads which produce more than one valid alignment with the same number of lowest
                mismatches or other reads that fail to align uniquely. (--output-suppressed-reads-r/l)" />
        <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false"
            label="Write all reads that could not be aligned to a file. (--output-unmapped-reads-r/l)" />

        <!-- output Options -->
        <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
        <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
        <!--end output options -->

    </xml>
    <xml name="citation">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btr167</citation>
        </citations>
    </xml>
</macros>