<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">7.520</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <!-- currently, the fasta3 executable is named according to its major version
    => needs updating together with the package requirement! -->
    <token name="@FASTA3_EXEC@">fasta36</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">MAFFT</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">mafft</requirement>
            <requirement type="package" version="36.3.8">fasta3</requirement>
        </requirements>
    </xml>
    <xml name="weighti_param">
        <param argument="--weighti" type="float" value="2.7" min="1" max="100" label="Weighting factor for the consistency term calculated from pairwise alignments."/>
    </xml>
    <xml name="parttree_parameters">
        <param argument="--retree" type="integer" value="2" min="1" max="3" label="Guide tree is built this number of times in the progressive stage."/>
        <param argument="--partsize" type="integer" value="50" min="0" max="1000" label="Number of partitions in the PartTree algorithm."/>
        <param argument="--groupsize" type="integer" value="-1" min="-1" label="Group size" help="Do not make alignment larger than this number of sequences. The default of -1 means set the value automatically to the number of input sequences."/>
    </xml>
    <xml name="misc_scoring_scheme">
        <param argument="--fmodel" type="boolean" truevalue="--fmodel" falsevalue="" checked="False" label="Incorporate the AA/nuc composition into the scoring matrix?" />
        <conditional name="gap_costs">
            <param name="use_defaults" type="select" label="Configure gap costs">
                <option value="yes">Use default values</option>
                <option value="no">Set values</option>
            </param>
            <when value="yes"/>
            <when value="no">
                <param argument="--ep" type="float" value="0.0" label="Gap extension penalty for group-to-group alignment" help="Offset value, which works like gap extension penalty, for group-to-group alignment."/>
                <param argument="--op" type="float" value="1.53" label="Gap opening penalty at group-to-group alignment." help="1.53 default value"/>
            </when>
        </conditional>
    </xml>
    <xml name="global_align_options">
        <section name="treat_unrelated_segments" title="Handling of unrelated segments in global alignments" expanded="true">
            <param argument="--unalignlevel" type="float" min="0" max="0.8" value="0" label="Over-alignment correction factor" help="The higher this factor the more likely will unrelated sequence stretches in globally related sequences be left unaligned. The default of 0 turns over-alignment correction off, turning it on increases run time."/>
            <param argument="--leavegappyregion" type="boolean" truevalue="--leavegappyregion" falsevalue="" label="Leave gappy region" help="Older option for preventing over-alignment by not trying to force gap-rich regions into an alignment. Can be used alone or in combination with the over-alignment correction factor, but has a much higher impact on run time and becomes less effective with more sequences. Not recommended for > ~1000 sequences."/>
        </section>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gkf436</citation>
            <citation type="doi">10.1093/nar/gki198</citation>
            <citation type="doi">10.1093/molbev/mst010</citation>
        </citations>
    </xml>
</macros>