<macros>
    <token name="@TOOL_VERSION@">0.6.7</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
        </requirements>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">trim_galore</xref>
        </xrefs>
    </xml>
    <xml name="adapter_trimming">
        <conditional name="trimming">
            <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
                <option value="">Automatic detection</option>
                <option value="--illumina">Illumina universal</option>
                <option value="--nextera">Nextera transposase</option>
                <option value="--small_rna">Illumina small RNA adapters</option>
                <option value="user">User defined adapter sequence</option>
            </param>
            <when value=""/>
            <when value="--illumina"/>
            <when value="--nextera"/>
            <when value="--small_rna"/>
            <when value="user">
                <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
                    <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
                </param>
                <yield/>
            </when>
        </conditional>
    </xml>
    <xml name="paired_adapter_trimming">
        <expand macro="adapter_trimming">
            <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2">
                <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
            </param>
        </expand>
        <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
        <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
                This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
                (--three_prime_clip_R1)</help>
        </param>
        <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2">
            <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after
                adapter/quality trimming has been performed. This may remove some unwanted bias from
                the 3' end that is not directly related to adapter sequence or basecall quality.</help>
        </param>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @misc{githubTrim_Galore,
                author = {Krueger, Felix},
                year = {2021},
                title = {Trim Galore},
                publisher = {GitHub},
                journal = {GitHub repository},
                url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
            </citation>        
        </citations>
    </xml>
</macros>