view g_forest.xml @ 5:0026cd452d0e draft default tip

planemo upload commit 72cee9103c0ae4acb5794afaed179bea2c729f2c-dirty

<tool id="g_forest" name="Compute Formants" version="0.01">
    <description>using wrassp formant tracker</description>

    <requirements>
        <requirement type="package" version="0.1.4">r-wrassp</requirement>
    </requirements>

    <command interpreter="bash">
        r_wrapper.sh $__tool_directory__/g_forest.R --args ${wavfile} ${output}
        ${beginTime} ${endTime} ${windowShift} ${windowSize} ${effectiveLength}
        ${nominalF1} ${gender} ${estimate} ${order} ${incrOrder} ${numFormants}
        ${window} ${preemphasis}
     </command>

     <stdio>
       <regex match="Linux: unexpected operator"
              source="stderr"
              level="warning"
              description="conda r-base bash bug" />
     </stdio>

    <inputs>
        <param name="wavfile" type="data" format="wav" label="Audio File" help="Audio file in WAV format"/>
        <param name="beginTime" type="integer" value="0" label="Start time for analysis (s)"/>
        <param name="endTime" type="integer" value="0" label="End Time for analysis (s) 0 means end of signal"/>
        <param name="windowShift" type="integer" value="5" label="Window Shift (ms)" help="set analysis window shift to dur ms"/>
        <param name="windowSize" type="integer" value="20" label="Window Size (ms)" help="set analysis window size to dur ms"/>
        <param name="effectiveLength" type="select" label="make window size effective rather than exact">
            <option value="1" selected="true">Yes</option>
            <option value="0">No</option>
        </param>
        <param name="nominalF1" type="integer" value="500" label="Nominal F1 Frequency (Hz)"/>
        <param name="gender" type="select" label="Speaker Gender">
            <option value="m" selected="true">Male</option>
            <option value="f">Female</option>
            <option value="u">Unknown</option>
        </param>
        <param name="estimate" type="select" label="Insert rough frequency estimates of missing formants (default: frequency set to zero)">
            <option value="1">Yes</option>
            <option value="0" selected="true">No</option>
        </param>
        <param name="order" type="integer" value="0" label="analysis order (default 0 means automatic)"/>
        <param name="incrOrder" type="integer" value="0" label="increment/decrement analysis order"/>
        <param name="numFormants" type="integer" value="4" label="Number of formants"/>
        <param name="window" type="select">
            <option value="BLACKMAN" selected="true">Blackman</option>
            <option value="RECTANGLE">rectangle</option>
            <option value="PARABOLA">parabola/Riesz/Welch</option>
            <option value="COS"      >cosine</option>
            <option value="HANN"     >Hann/hanning/cosine^2</option>
            <option value="COS_4"    >cosine^4</option>
            <option value="HAMMING"  >Hamming</option>
            <option value="BLACK_X"  >exact Blackman</option>
            <option value="BLACK_M3" >min. 3-term Blackman-Nuttal</option>
            <option value="BLACK_M4" >min. 4-term Blackman-Nuttal</option>
            <option value="NUTTAL_3" >3-term Nuttal (-18 dB/oct)</option>
            <option value="NUTTAL_4" >4-term Nuttal (-18 dB/oct)</option>
            <option value="KAISER2_0">Kaiser-Bessel (alpha = 2.0)</option>
            <option value="KAISER3_0">Kaiser-Bessel (alpha = 3.0)</option>
            <option value="KAISER4_0">Kaiser-Bessel (alpha = 4.0)</option>
        </param>
        <param name="preemphasis" type="float" value="-0.8" min="-1" max="0" label="Pre-emphasis"/>
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="#echo $wavfile.element_identifier.replace('wav', 'fm') #" />
    </outputs>


    <tests>
        <test>
            <param name="wavfile" value="1_1119_2_22_001-ch6-speaker16.wav"/>
            <output name="output" file="1_1119_2_22_001-formants.dat"/>
        </test>
    </tests>

    <help>Calculate the formant tracks for segments of an audio file.
 Raw resonance frequency and bandwidth values are obtained by root-solving of the Linear Prediction polynomial from the autocorrelation method and the Split-Levinson-Algorithm (SLA). Resonances are then classified as formants using the so-called Pisarenko frequencies (by-product of the SLA) and a formant frequeny range table derived from the nominal F1 frequency. The latter may have to be increased by about 12% for female voices (see NominalF1 and Gender options).
    </help>

    <citations>
        <citation type='bibtex'>
            @Manual{,
              title = {wrassp: an R wrapper to the ASSP Library},
              author = {Lasse Bombien and Raphael Winkelmann and Michel
                Scheffers},
              year = {2016},
              note = {R package version 0.1.4},
            }
        </citation>
    </citations>
</tool>