<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">trinity</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">trinity</xref>
        </xrefs>
    </xml>
    <token name="@TOOL_VERSION@">2.15.1</token>
    <token name="@VERSION_SUFFIX@">0</token>

    <token name="@COMMAND_PAIRED_STRAND_JACCARD@">
        #if $pool.inputs.strand.is_strand_specific == 'true':
            --SS_lib_type $pool.inputs.strand.library_type
        #end if

        $pool.inputs.jaccard_clip
    </token>

    <xml name="input_paired_strand_jaccard">
        <conditional name="strand">
            <param name="is_strand_specific" type="select" label="Strand specific data">
                <option value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false" />
            <when value="true">
                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type">
                    <option value="FR">Forward-Reverse</option>
                    <option value="RF">Reverse-Forward</option>
                </param>
            </when>
        </conditional>
        <param argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/>
    </xml>

    <xml name="is_strand_specific_f_r">
        <conditional name="strand">
            <param name="is_strand_specific" type="select" label="Strand specific data">
                <option value="false">No</option>
                <option value="true">Yes</option>
            </param>
            <when value="false"/>
            <when value="true">
                <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type">
                    <option value="F">F</option>
                    <option value="R">R</option>
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1038/nbt.1883</citation>
        </citations>
    </xml>
</macros>