<macros>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">edta</xref>
        </xrefs>
    </xml>
    <xml name="edta_main_param">
        <!-- Genome to TE annotations -->
        <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
        <param argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
            <option value="Others">Others</option>
            <option value="Rice">Rice</option>
            <option value="Maize">Maize</option>
        </param>
        <param argument="--step" type="select" label="Specify which steps you want to run EDTA">
            <option value="all">run the entire pipeline (all)</option>
            <option value="filter"> start from raw TEs to the end (filter)</option>
            <option value="final">Final</option>
            <option value="anno">Anno</option>
        </param>
        <param argument="--cds" type="data" format="fasta" label="Coding Sequence File" optional='true' help="Provide a FASTA file containing the coding sequence (no introns, UTRs, nor TEs) of this genome or its close relative."/> 
        <param argument="--curatedlib" type="data" format="fasta" label="Curated Library File" optional='true' help="Provided a curated library to keep consistant naming and classification for known TEs. All TEs in this file will be trusted 100%, so please ONLY provide MANUALLY CURATED ones here."/>
        <param argument="--sensitive" type="boolean"  truevalue="--sensitive 1" falsevalue=""  label="Use RepeatModeler to identify remaining TEs" help="Use RepeatModeler to identify remaining TEs This step is very slow and MAY help to recover some TEs."/>
        <param name="mutation_rate" argument="--u" type="float" optional="True" label="Neutral Mutation Rate" help="Neutral mutation rate to calculate the age of intact LTR elements. Default: 1.3e-8 (per bp per year, from rice)"></param>
        <conditional name='anno_select'>
            <param name="anno" type="select" label="Would you like to perform whole-genome TE annotation after TE library construction?" argument='--a' help='Perform or not perform whole-genome TE annotation after TE library construction.'>
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="Evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
                <param name="exclude" argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
            </when>
            <when value="no"></when>
        </conditional>
    </xml>
    <xml name="pan_edta">
        <!-- Genome to TE annotations -->
        <param name="known_te" type='data' format="fasta" label="Genome File" optional='true' help="File of known TEs"></param>
        <repeat name="te_library" title="TE_Library">
            <param argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
            <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
                <option value="Others">Others</option>
                <option value="Rice">Rice</option>
                <option value="Maize">Maize</option>
            </param>
            <param argument="--cds" type="data" format="fasta" label="Coding Sequence File" optional='true' help="Provide a FASTA file containing the coding sequence (no introns, UTRs, nor TEs) of this genome or its close relative."/> 
            <param argument="--curatedlib" type="data" format="fasta" label="Curated Library File" optional='true' help="Provided a curated library to keep consistant naming and classification for known TEs. All TEs in this file will be trusted 100%, so please ONLY provide MANUALLY CURATED ones here."/>
            <param argument="--sensitive" type="boolean"  truevalue="--sensitive 1" falsevalue=""  label="Use RepeatModeler to identify remaining TEs" help="Use RepeatModeler to identify remaining TEs This step is very slow and MAY help to recover some TEs."/>
            <param name="mutation_rate" argument="--u" type="float" optional="True" label="Neutral Mutation Rate" help="Neutral mutation rate to calculate the age of intact LTR elements. Default: 1.3e-8 (per bp per year, from rice)"></param>
            <param argument="--evaluate" type="boolean" truevalue="--evaluate 1" falsevalue="" label="evaluate" help="Evaluate (1) classification consistency of the TE annotation " />
            <param argument="--exclude" type="data" format="bed" label="Exclude" help="Exclude bed format regions from TE annotation" optional="true"/>
        </repeat> 
    </xml>
    <xml name="te_only">
        <!-- Find elements of a paticular TE type -->
        <param name="genome" argument="--genome" type="data" format="fasta" label="Genome File" help="The Genome FASTA file"/>
        <param name='species' argument ="--species" type="select" label="Which species should be used for identification of TIR candidates">
            <option value="Others">Others</option>
            <option value="Rice">Rice</option>
            <option value="Maize">Maize</option>
        </param>
        <param name="te_type" argument="--type" type="select" label="Which type of raw TE candidates do you want?">
            <option value="all">all</option>
            <option value="ltr">ltr</option>
            <option value="tir">tir</option>
            <option value="helitron">helitron</option>
        </param>
    </xml>
</macros>