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<tool id="vowel_plot" name="Plot Vowels" version="0.01" force_history_refresh="True">
    <description>Using phonR to produce a Vowel Plot</description>

    <requirements>
        <requirement type="package" version="1.0_3">r-phonr</requirement>
        <requirement type="package">r-getopt</requirement>
    </requirements>

    <command interpreter="Rscript">
        $__tool_directory__/phonR_tool.R --input="${input}"  --pdffile="$pdffile" --column1="${f1}" --column2="${f2}" --columnvowels="${vowel}" --pretty="${pretty}" --ellipse="${ellipse}" --tokens="${tokens}" --means="${means}" --cextokens="${cextokens}" --alphatokens="${alphatokens}" --cexmeans="${cexmeans}"
    </command>
    
    <stdio>
      <regex match="Linux: unexpected operator"
             source="stderr"
             level="warning"
             description="conda r-base bash bug" />
    </stdio>

    <inputs>
        <param name="input" type="data" format="tabular" label="Segment List" help=""/>
        <param name="f1" type="data_column" data_ref="input" label="Column for f1" force_select="true" use_header_names="true"/>
        <param name="f2" type="data_column" data_ref="input" label="Column for f2" force_select="true" use_header_names="true"/>
        <param name="vowel" type="data_column" data_ref="input" label="Column with Vowels" force_select="true" use_header_names="true"/>
        <param name="pretty" type="boolean" label="Make Pretty"
               truevalue="TRUE" falsevalue="FALSE" checked="True"
               help="Will apply various beautification techniques." />
        <param name="ellipse" type="boolean" label="Add Ellipses"
               truevalue="TRUE" falsevalue="FALSE" checked="True"
               help="Will add an ellipse around the location of each vowel cluster." />
        <param name="tokens" type="boolean" label="Add Tokens"
               truevalue="TRUE" falsevalue="FALSE" checked="True"
               help="Will add tokens to the plot." />
        <param name="means" type="boolean" label="Add Means"
               truevalue="TRUE" falsevalue="FALSE" checked="True"
               help="Will add means to the plot." />
        <param name="cextokens" type="float" label="cex.tokens" value="1.2" min="0.0" max="10.0"
               help="Size of tokens on the plot." />
        <param name="alphatokens" type="float" label="alpha.tokens" value="0.2" min="0.0" max="1.0"
               help="The alpha of the tokens on the plot (transparency). NOTE: Must be a value betweek 0 and 1!" />
        <param name="cexmeans" type="float" label="cex.means" value="2" min="0.0" max="10.0"
               help="Size of the means on the plot." />
    </inputs>

    <outputs>
        <data format="pdf" name="pdffile" label="vowelplot.pdf" />
    </outputs>


    <tests>
        <test>
            <param name="input" value="femaletest.tsv"/>
            <param name="f1" value='4' />
            <param name="f2" value='5' />
            <param name="vowel" value='3'/>
            <output name="output" file="femalevowelplot.pdf" compare="sim_size" />
        </test>
    </tests>

    <help>
        Will make a vowel plot from given data. Best used from data directly run from the "Get Formants at segment midpoint" Tool.
    </help>

</tool>