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annotate phonR_tool.xml @ 1:4c17593167f0 draft

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author stevecassidy
date Thu, 13 Oct 2016 15:41:12 -0400
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1 <tool id="vowel_plot" name="Plot Vowels" version="0.01" force_history_refresh="True">
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2 <description>Using phonR to produce a Vowel Plot</description>
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3
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4 <requirements>
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5 <requirement type="package" version="3.2.1">R</requirement>
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6 <requirement type="package" version="1.0_3">r-phonr</requirement>
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7 </requirements>
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8
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9 <command interpreter="Rscript">
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10 $__tool_directory__/phonR_tool.R --input="${input}" --outdir="$htmlfile.files_path" --htmlfile="$htmlfile" --column1="${f1}" --column2="${f2}" --columnvowels="${vowel}" --pretty="${pretty}" --ellipse="${ellipse}" --tokens="${tokens}" --means="${means}" --cextokens="${cextokens}" --alphatokens="${alphatokens}" --cexmeans="${cexmeans}"
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11 </command>
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12
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Segment List" help=""/>
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15 <param name="f1" type="data_column" data_ref="input" label="Column for f1" force_select="true" use_header_names="true"/>
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16 <param name="f2" type="data_column" data_ref="input" label="Column for f2" force_select="true" use_header_names="true"/>
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17 <param name="vowel" type="data_column" data_ref="input" label="Column with Vowels" force_select="true" use_header_names="true"/>
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18 <param name="pretty" type="boolean" label="Make Pretty"
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19 truevalue="TRUE" falsevalue="FALSE" checked="True"
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20 help="Will apply various beautification techniques." />
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21 <param name="ellipse" type="boolean" label="Add Ellipses"
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22 truevalue="TRUE" falsevalue="FALSE" checked="True"
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23 help="Will add an ellipse around the location of each vowel cluster." />
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24 <param name="tokens" type="boolean" label="Add Tokens"
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25 truevalue="TRUE" falsevalue="FALSE" checked="True"
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26 help="Will add tokens to the plot." />
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27 <param name="means" type="boolean" label="Add Means"
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28 truevalue="TRUE" falsevalue="FALSE" checked="True"
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29 help="Will add means to the plot." />
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30 <param name="cextokens" type="float" label="cex.tokens" value="1.2" min="0.0" max="10.0"
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31 help="Size of tokens on the plot." />
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32 <param name="alphatokens" type="float" label="alpha.tokens" value="0.2" min="0.0" max="1.0"
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33 help="The alpha of the tokens on the plot (transparency). NOTE: Must be a value betweek 0 and 1!" />
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34 <param name="cexmeans" type="float" label="cex.means" value="2" min="0.0" max="10.0"
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35 help="Size of the means on the plot." />
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36 </inputs>
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37
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38 <outputs>
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39 <data format="html" name="htmlfile" label="output.html" />
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40 </outputs>
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41
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42
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43 <tests>
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44 <test>
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45 <param name="input" value="femaletest.tsv"/>
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46 <param name="f1" value=4/>
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47 <param name="f2" value=5/>
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48 <param name="vowel" value="vowel"/>
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49 <output name="output">
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50 <assert_contents>
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51 <has_text text="html"/>
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52 </assert_contents>
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53 </output>
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54 </test>
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55 </tests>
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56
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57 <help>
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58 Will make a vowel plot from given data. Best used from data directly run from the "Get Formants at segment midpoint" Tool.
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59 </help>
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60
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61 </tool>