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<tool id="maus_bpf" name="MAUS Align" version="0.01" force_history_refresh="True">
    <description>from BPF transcription</description>

    <requirements>
        <container type="docker">stevecassidy/maus</container>
    </requirements>

    <command>
        ln -s "${signal}" input.wav &amp;&amp;
        /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
        BPF=$bpf INSKANTEXTGRID=$inskantextgrid INSORTTEXTGRID=$insorttextgrid
        MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen WEIGHT=$weight
        INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence OUTSYMBOL=$outsymbol
        OUT=$output SIGNAL=input.wav
    </command>

    <inputs>
        <param name="signal" type="data" format="wav" label="Audio File"/>
        <param name="bpf" type="data" format="par" label="BPF File" help="Orthographic Transcript as BPF"/>
        <param name="language" type="select" label="Language">
            <option value="aus">Australian English</option>
            <option value="sampa">SAMPA</option>
            <option value="deu">Germa</option>
            <option value="gsw-CH">Swiss German</option>
            <option value="eng">British English</option>
            <option value="fin">Finnish</option>
            <option value="fra">French</option>
            <option value="eng-US">US English</option>
            <option value="nld">Dutch</option>
            <option value="spa">Spanish</option>
            <option value="ita">Italian</option>
            <option value="por">Portugese</option>
            <option value="hun">Hungarian</option>
            <option value="ekk">Estonian</option>
            <option value="pol">Polish</option>
            <option value="nze">NZ English</option>
            <option value="kat">Georgian</option>
            <option value="rus">Russian</option>
        </param>
        <param name="insorttextgrid" type="boolean" value="true" label="Add Orthography to TextGrid output"/>
        <param name="inskantextgrid" type="boolean" value="true" label="Add canonical phonemic transcription to TextGrid output"/>
        <param name="modus" type="select" label="Mode">
            <option value="standard">Normal MAUS technique</option>
            <option value="align">Do not model pronunciation, align the given phonemic transcript</option>
            <option value="bigram">Use phone recognition constrained by a Bigram model</option>
        </param>
        <param name="mausshift" type="integer" value="10" label="Shift found segment boundaries by this many milliseconds"/>
        <param name="minpauslen" type="integer" label="supress inter-word silence less than n*10ms, ie. enter 5 here to suppress silence less than 50ms" value='5'/>
        <param name="weight" type="float" value="7.0" label="relative weight given to statistical model, higher values will favour the canonical pronunciation"/>
        <param name="insprob" type="float" value="0.0" label="Insertion probability - higher values will reduce the probability of deletions of phonemic segments"/>
        <param name="noinitialfinalsilence" type="select" label="Suppress initial and final silence">
            <option value="no">No</option>
            <option value="yes">Yes</option>
        </param>
        <param name="outsymbol" type="select" label="Output symbols">
            <option value="sampa">SAMPA</option>
            <option value="ipa">IPA (utf-8)</option>
            <option value="manner">IPA manner class</option>
            <option value="place">IPA place of articulation</option>
        </param>
    </inputs>

    <outputs>
        <data name="output" format="textgrid" label="#echo $signal.element_identifier.replace('.wav', '.TextGrid') #" />
    </outputs>


    <tests>
        <test>
            <param name="signal" type="wav" value="1_1119_2_22_001-ch6-speaker16.wav"/>
            <param name="bpf" value="1_1119_2_22_001.par"/>
            <param name="language" value="aus"/>
            <param name="insorttextgrid" value="true" />
            <param name="inskantextgrid" value="true" />
            <output name="output" file="1_1119_2_22_001.TextGrid"/>
        </test>
    </tests>

    <help>Run the MAUS forced aligner on an audio file given a transcription in BPF format.
    Output is a TextGrid file containing the phonemic annotation with start/end times for each
    segment.</help>

    <citations>
        <citation type='bibtex'>
            @inproceedings{Strunk2011,
            booktitle = {Proceedings of the Ninth International Conference on Language Resources and Evaluation},
            publisher = {European Language Resources Association (ELRA)},
            isbn = {978-2-9517408-8-4},
            keywords = {forced alignment,language documentation corpora,word times},
            title = {{Untrained Forced Alignment of Transcriptions and Audio for Language Documentation Corpora using WebMAUS}},
            url = {http://www.bas.uni-muenchen.de/forschung/publikationen/Schiel-LREC2014.pdf},
            year = {2014}
            }
        </citation>
    </citations>
</tool>