Mercurial > repos > stevecassidy > vowelplot

annotate phonR_tool.xml @ 4:0c6aea9fe490 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
author stevecassidy
date Wed, 14 Dec 2016 21:54:31 -0500
parents 24f05f509f09
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
1 <tool id="vowel_plot" name="Plot Vowels" version="0.01" force_history_refresh="True">
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
2 <description>Using phonR to produce a Vowel Plot</description>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
3
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
4 <requirements>
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
5 <requirement type="package" version="1.0_3">r-phonr</requirement>
2
3e7b945648a4 planemo upload commit 872df0b3bcaa92f0cac12cd46d4f2fa6de261293-dirty
stevecassidy
parents: 1
diff changeset
6 <requirement type="package">r-getopt</requirement>
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
7 </requirements>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
8
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
9 <command interpreter="Rscript">
3
24f05f509f09 planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
stevecassidy
parents: 2
diff changeset
10 $__tool_directory__/phonR_tool.R --input="${input}" --pdffile="$pdffile" --column1="${f1}" --column2="${f2}" --columnvowels="${vowel}" --pretty="${pretty}" --ellipse="${ellipse}" --tokens="${tokens}" --means="${means}" --cextokens="${cextokens}" --alphatokens="${alphatokens}" --cexmeans="${cexmeans}"
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
11 </command>
4
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
12
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
13 <stdio>
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
14 <regex match="Linux: unexpected operator"
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
15 source="stderr"
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
16 level="warning"
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
17 description="conda r-base bash bug" />
0c6aea9fe490 planemo upload commit 2d22bc12c66a3d1949d4bf4c84e7ce7c4610383c-dirty
stevecassidy
parents: 3
diff changeset
18 </stdio>
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
19
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
20 <inputs>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
21 <param name="input" type="data" format="tabular" label="Segment List" help=""/>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
22 <param name="f1" type="data_column" data_ref="input" label="Column for f1" force_select="true" use_header_names="true"/>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
23 <param name="f2" type="data_column" data_ref="input" label="Column for f2" force_select="true" use_header_names="true"/>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
24 <param name="vowel" type="data_column" data_ref="input" label="Column with Vowels" force_select="true" use_header_names="true"/>
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
25 <param name="pretty" type="boolean" label="Make Pretty"
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
26 truevalue="TRUE" falsevalue="FALSE" checked="True"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
27 help="Will apply various beautification techniques." />
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
28 <param name="ellipse" type="boolean" label="Add Ellipses"
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
29 truevalue="TRUE" falsevalue="FALSE" checked="True"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
30 help="Will add an ellipse around the location of each vowel cluster." />
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
31 <param name="tokens" type="boolean" label="Add Tokens"
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
32 truevalue="TRUE" falsevalue="FALSE" checked="True"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
33 help="Will add tokens to the plot." />
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
34 <param name="means" type="boolean" label="Add Means"
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
35 truevalue="TRUE" falsevalue="FALSE" checked="True"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
36 help="Will add means to the plot." />
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
37 <param name="cextokens" type="float" label="cex.tokens" value="1.2" min="0.0" max="10.0"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
38 help="Size of tokens on the plot." />
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
39 <param name="alphatokens" type="float" label="alpha.tokens" value="0.2" min="0.0" max="1.0"
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
40 help="The alpha of the tokens on the plot (transparency). NOTE: Must be a value betweek 0 and 1!" />
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
41 <param name="cexmeans" type="float" label="cex.means" value="2" min="0.0" max="10.0"
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
42 help="Size of the means on the plot." />
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
43 </inputs>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
44
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
45 <outputs>
3
24f05f509f09 planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
stevecassidy
parents: 2
diff changeset
46 <data format="pdf" name="pdffile" label="vowelplot.pdf" />
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
47 </outputs>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
48
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
49
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
50 <tests>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
51 <test>
1
4c17593167f0 planemo upload commit 8787f5af57672a8fd5311e206b872833c8b3fede-dirty
stevecassidy
parents: 0
diff changeset
52 <param name="input" value="femaletest.tsv"/>
2
3e7b945648a4 planemo upload commit 872df0b3bcaa92f0cac12cd46d4f2fa6de261293-dirty
stevecassidy
parents: 1
diff changeset
53 <param name="f1" value='4' />
3e7b945648a4 planemo upload commit 872df0b3bcaa92f0cac12cd46d4f2fa6de261293-dirty
stevecassidy
parents: 1
diff changeset
54 <param name="f2" value='5' />
3
24f05f509f09 planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
stevecassidy
parents: 2
diff changeset
55 <param name="vowel" value='3'/>
24f05f509f09 planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
stevecassidy
parents: 2
diff changeset
56 <output name="output" file="femalevowelplot.pdf" compare="sim_size" />
0
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
57 </test>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
58 </tests>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
59
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
60 <help>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
61 Will make a vowel plot from given data. Best used from data directly run from the "Get Formants at segment midpoint" Tool.
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
62 </help>
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
63
3d068b7441be planemo upload commit f36456464c692ed9d39a9cf654d09fe793113cce-dirty
stevecassidy
parents:
diff changeset
64 </tool>