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"planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5fd9687d543a48a715b1180caf93abebebd58b0e"
author eschen42
date Wed, 18 Nov 2020 18:53:37 +0000
parents 2ae2d26e3270
children
comparison
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13:2ae2d26e3270 14:90708fdbc22d
1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.17"> 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.18">
2 <description>OPLS-DA Contrasts of Univariate Results</description> 2 <description>OPLS-DA Contrasts of Univariate Results</description>
3 <macros> 3 <macros>
4 <xml name="paramPairSigFeatOnly"> 4 <xml name="paramPairSigFeatOnly">
5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" 5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
6 label="Retain only pairwise-significant features" 6 label="Retain only pairwise-significant features"
23 </xml> 23 </xml>
24 </macros> 24 </macros>
25 <requirements> 25 <requirements>
26 <requirement type="package">r-base</requirement> 26 <requirement type="package">r-base</requirement>
27 <requirement type="package">r-batch</requirement> 27 <requirement type="package">r-batch</requirement>
28 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement> 28 <requirement type="package" version="1.22.0">bioconductor-ropls</requirement>
29 </requirements> 29 </requirements>
30 <command detect_errors="aggressive"><![CDATA[ 30 <command detect_errors="aggressive"><![CDATA[
31 Rscript '$__tool_directory__/w4mcorcov_wrapper.R' 31 Rscript '$__tool_directory__/w4mcorcov_wrapper.R'
32 dataMatrix_in '$dataMatrix_in' 32 dataMatrix_in '$dataMatrix_in'
33 sampleMetadata_in '$sampleMetadata_in' 33 sampleMetadata_in '$sampleMetadata_in'
55 cplot_y '$advanced.cplot_y' 55 cplot_y '$advanced.cplot_y'
56 #end if 56 #end if
57 contrast_detail '$contrast_detail' 57 contrast_detail '$contrast_detail'
58 contrast_corcov '$contrast_corcov' 58 contrast_corcov '$contrast_corcov'
59 contrast_salience '$contrast_salience' 59 contrast_salience '$contrast_salience'
60 min_crossval_i '$min_crossval_i'
60 ]]></command> 61 ]]></command>
61 <inputs> 62 <inputs>
62 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data" 63 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
63 help="variables &#10006; samples" /> 64 help="variables &#10006; samples" />
64 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data" 65 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
133 <option value="regex">use regular expressions for matching level-names</option> 134 <option value="regex">use regular expressions for matching level-names</option>
134 </param> 135 </param>
135 <param name="labelFeatures" type="text" value="3" 136 <param name="labelFeatures" type="text" value="3"
136 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot?" 137 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot?"
137 help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/> 138 help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>
139 <param name="min_crossval_i" type="text" value="7"
140 label="Minumum number of samples for OPLS-DA cross-validation."
141 help="What is the minimum number of samples to be used by the ropls package for cross-validation of OPLS-DA predictions? This should be not more than half the number of your samples."/>
138 <conditional name="advanced"> 142 <conditional name="advanced">
139 <param name="advancedFeatures" type="select" 143 <param name="advancedFeatures" type="select"
140 label="Advanced (C-plots and customized p-value adjustment)" 144 label="Advanced (C-plots and customized p-value adjustment)"
141 help="Choose 'Do not include ...' to hides further choices."> 145 help="Choose 'Do not include ...' to hides further choices.">
142 <option value="advanced">Include C-plots and customize p-value adjustment.</option> 146 <option value="advanced">Include C-plots and customize p-value adjustment.</option>
177 * Salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels. 181 * Salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels.
178 --> 182 -->
179 <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" /> 183 <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" />
180 </outputs> 184 </outputs>
181 <tests> 185 <tests>
182 <!-- test #1 --> 186 <!-- test #1 - issue 14 -->
187 <test>
188 <param name="dataMatrix_in" value="issue14_input_dataMatrix.tsv"/>
189 <param name="sampleMetadata_in" value="issue14_input_sampleMetadata.tsv"/>
190 <param name="variableMetadata_in" value="issue14_input_variableMetadata.tsv"/>
191 <param name="tesC" value="none"/>
192 <param name="facC" value="tissue_flowering"/>
193 <param name="labelFeatures" value="3"/>
194 <param name="min_crossval_i" value="4"/>
195 <param name="fdr_features" value="ALL"/>
196 <param name="levCSV" value="*"/>
197 <param name="matchingC" value="wildcard"/>
198 <output name="contrast_corcov">
199 <assert_contents>
200 <!-- column-labels line -->
201 <has_text text="featureID" />
202 <has_text text="factorLevel1" />
203 <has_text text="factorLevel2" />
204 <has_text text="correlation" />
205 <has_text text="covariance" />
206 <has_text text="vip4p" />
207 <has_text text="vip4o" />
208 <!-- a matched line -->
209 <has_text text="NM516T283_1" />
210 <has_text text="flower_yes" />
211 <has_text text="leaf_no" />
212 <has_text text="-0.98475578586" />
213 <has_text text="-58.1219648" />
214 <has_text text="2.0103501" />
215 <has_text text="2.872672881" />
216 <has_text text="-0.1208407903" />
217 <has_text text="-0.2032249" />
218 <has_text text="-0.9857575" />
219 <has_text text="-0.983684189899" />
220 <has_text text="516.080116" />
221 <has_text text="282.50076" />
222 </assert_contents>
223 </output>
224 </test>
225 <!-- test #2 - issue 6 -->
226 <test>
227 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
228 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
229 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
230 <param name="tesC" value="none"/>
231 <param name="facC" value="k._10"/>
232 <param name="labelFeatures" value="3"/>
233 <param name="min_crossval_i" value="7"/>
234 <param name="fdr_features" value="ALL"/>
235 <param name="levCSV" value="k_3,k-4"/>
236 <param name="matchingC" value="none"/>
237 <output name="contrast_corcov">
238 <assert_contents>
239 <!-- column-labels line -->
240 <has_text text="featureID" />
241 <has_text text="factorLevel1" />
242 <has_text text="factorLevel2" />
243 <has_text text="correlation" />
244 <has_text text="covariance" />
245 <has_text text="vip4p" />
246 <has_text text="vip4o" />
247 <!-- first matched line -->
248 <has_text text="M349.2383T700" />
249 <has_text text="-0.1221966" />
250 <has_text text="-917311734" />
251 <has_text text="0.0304592" />
252 <has_text text="0.104748883" />
253 <has_text text="-0.002736415" />
254 <has_text text="-0.0113968" />
255 <has_text text="0.387723" />
256 <has_text text="-0.3812168081" />
257 <has_text text="0.154611878" />
258 </assert_contents>
259 </output>
260 </test>
261 <!-- test #3 - issue 8 -->
262 <test>
263 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
264 <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/>
265 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
266 <param name="tesC" value="none"/>
267 <param name="facC" value="k._10"/>
268 <param name="labelFeatures" value="3"/>
269 <param name="min_crossval_i" value="7"/>
270 <param name="fdr_features" value="ALL"/>
271 <param name="levCSV" value="k_3,k-4"/>
272 <param name="matchingC" value="none"/>
273 <output name="contrast_corcov">
274 <assert_contents>
275 <!-- column-labels line -->
276 <has_text text="featureID" />
277 <has_text text="factorLevel1" />
278 <has_text text="factorLevel2" />
279 <has_text text="correlation" />
280 <has_text text="covariance" />
281 <has_text text="vip4p" />
282 <has_text text="vip4o" />
283 <!-- k1 rejected by levCSV, leaving only k_3 and k-4 -->
284 <not_has_text text="k1" />
285 <not_has_text text="other" />
286 <!-- first matched line -->
287 <has_text text="M200.005T296" />
288 <has_text text="-0.1829149760" />
289 <has_text text="-115723402" />
290 <has_text text="0.0892595" />
291 <has_text text="0.00492288" />
292 <has_text text="-0.00801895" />
293 <has_text text="0.0005356178" />
294 <has_text text="0.1848186" />
295 <has_text text="-0.428802311" />
296 <has_text text="0.0882045811" />
297 </assert_contents>
298 </output>
299 </test>
300 <!-- test #4 -->
183 <test> 301 <test>
184 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 302 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
185 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 303 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
186 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 304 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
187 <param name="tesC" value="kruskal"/> 305 <param name="tesC" value="kruskal"/>
188 <param name="facC" value="k10"/> 306 <param name="facC" value="k10"/>
189 <param name="pairSigFeatOnly" value="FALSE"/> 307 <param name="pairSigFeatOnly" value="FALSE"/>
190 <param name="labelFeatures" value="3"/> 308 <param name="labelFeatures" value="3"/>
309 <param name="min_crossval_i" value="7"/>
191 <param name="fdr_features" value="250"/> 310 <param name="fdr_features" value="250"/>
192 <param name="levCSV" value="k[12],k[3-4]"/> 311 <param name="levCSV" value="k[12],k[3-4]"/>
193 <param name="matchingC" value="regex"/> 312 <param name="matchingC" value="regex"/>
194 <output name="contrast_corcov"> 313 <output name="contrast_corcov">
195 <assert_contents> 314 <assert_contents>
239 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" /> 358 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
240 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" /> 359 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
241 </assert_contents> 360 </assert_contents>
242 </output> 361 </output>
243 </test> 362 </test>
244 <!-- test #2 --> 363 <!-- test #5 -->
245 <test> 364 <test>
246 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 365 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
247 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 366 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
248 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 367 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
249 <param name="tesC" value="kruskal"/> 368 <param name="tesC" value="kruskal"/>
250 <param name="facC" value="k10"/> 369 <param name="facC" value="k10"/>
251 <param name="pairSigFeatOnly" value="TRUE"/> 370 <param name="pairSigFeatOnly" value="TRUE"/>
252 <param name="labelFeatures" value="3"/> 371 <param name="labelFeatures" value="3"/>
372 <param name="min_crossval_i" value="7"/>
253 <param name="fdr_features" value="ALL"/> 373 <param name="fdr_features" value="ALL"/>
254 <param name="levCSV" value="k[12],k[3-4]"/> 374 <param name="levCSV" value="k[12],k[3-4]"/>
255 <param name="matchingC" value="regex"/> 375 <param name="matchingC" value="regex"/>
256 <output name="contrast_corcov"> 376 <output name="contrast_corcov">
257 <assert_contents> 377 <assert_contents>
284 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" /> 404 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
285 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" /> 405 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
286 </assert_contents> 406 </assert_contents>
287 </output> 407 </output>
288 </test> 408 </test>
289 <!-- test #3 --> 409 <!-- test #6 -->
290 <test> 410 <test>
291 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 411 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
292 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 412 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
293 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 413 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
294 <param name="tesC" value="none"/> 414 <param name="tesC" value="none"/>
295 <param name="facC" value="k10"/> 415 <param name="facC" value="k10"/>
296 <param name="labelFeatures" value="3"/> 416 <param name="labelFeatures" value="3"/>
417 <param name="min_crossval_i" value="7"/>
297 <param name="fdr_features" value="ALL"/> 418 <param name="fdr_features" value="ALL"/>
298 <param name="levCSV" value="k[12],k[3-4]"/> 419 <param name="levCSV" value="k[12],k[3-4]"/>
299 <param name="matchingC" value="regex"/> 420 <param name="matchingC" value="regex"/>
300 <output name="contrast_corcov"> 421 <output name="contrast_corcov">
301 <assert_contents> 422 <assert_contents>
333 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" /> 454 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
334 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" /> 455 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
335 </assert_contents> 456 </assert_contents>
336 </output> 457 </output>
337 </test> 458 </test>
338 <!-- test #4 --> 459 <!-- test #7 -->
339 <test> 460 <test>
340 <param name="dataMatrix_in" value="issue1_input_dataMatrix.tsv"/> 461 <param name="dataMatrix_in" value="issue1_input_dataMatrix.tsv"/>
341 <param name="sampleMetadata_in" value="issue1_input_sampleMetadata.tsv"/> 462 <param name="sampleMetadata_in" value="issue1_input_sampleMetadata.tsv"/>
342 <param name="variableMetadata_in" value="issue1_input_variableMetadata.tsv"/> 463 <param name="variableMetadata_in" value="issue1_input_variableMetadata.tsv"/>
343 <param name="tesC" value="none"/> 464 <param name="tesC" value="none"/>
344 <param name="facC" value="tissue_flowering"/> 465 <param name="facC" value="tissue_flowering"/>
345 <param name="labelFeatures" value="3"/> 466 <param name="labelFeatures" value="3"/>
467 <param name="min_crossval_i" value="7"/>
346 <param name="fdr_features" value="ALL"/> 468 <param name="fdr_features" value="ALL"/>
347 <param name="levCSV" value="*"/> 469 <param name="levCSV" value="*"/>
348 <param name="matchingC" value="wildcard"/> 470 <param name="matchingC" value="wildcard"/>
349 <output name="contrast_corcov"> 471 <output name="contrast_corcov">
350 <assert_contents> 472 <assert_contents>
384 <has_text text="NM517T426_1" /><has_text text="0.0290065" /><has_text text="7.7151305" /><has_text text="1.2758886" /><has_text text="517.09367125" /><has_text text="426.233886719" /> 506 <has_text text="NM517T426_1" /><has_text text="0.0290065" /><has_text text="7.7151305" /><has_text text="1.2758886" /><has_text text="517.09367125" /><has_text text="426.233886719" />
385 <has_text text="NM516T284_2" /><has_text text="0.022883902" /><has_text text="7.6379724" /><has_text text="1.25603610" /><has_text text="516.082005177" /><has_text text="283.569198608" /> 507 <has_text text="NM516T284_2" /><has_text text="0.022883902" /><has_text text="7.6379724" /><has_text text="1.25603610" /><has_text text="516.082005177" /><has_text text="283.569198608" />
386 </assert_contents> 508 </assert_contents>
387 </output> 509 </output>
388 </test> 510 </test>
389 <!-- test #5 --> 511 <!-- test #8 -->
390 <test> 512 <test>
391 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 513 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
392 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/> 514 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
393 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 515 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
394 <param name="tesC" value="none"/> 516 <param name="tesC" value="none"/>
395 <param name="facC" value="k._10"/> 517 <param name="facC" value="k._10"/>
396 <param name="labelFeatures" value="3"/> 518 <param name="labelFeatures" value="3"/>
519 <param name="min_crossval_i" value="7"/>
397 <param name="fdr_features" value="ALL"/> 520 <param name="fdr_features" value="ALL"/>
398 <param name="levCSV" value="k1,k.2"/> 521 <param name="levCSV" value="k1,k.2"/>
399 <param name="matchingC" value="none"/> 522 <param name="matchingC" value="none"/>
400 <output name="contrast_corcov"> 523 <output name="contrast_corcov">
401 <assert_contents> 524 <assert_contents>
417 <has_text text="M207.9308T206" /> 540 <has_text text="M207.9308T206" />
418 <has_text text="-0.89716403" /> 541 <has_text text="-0.89716403" />
419 <has_text text="-585563327.7" /> 542 <has_text text="-585563327.7" />
420 <has_text text="0.270297" /> 543 <has_text text="0.270297" />
421 <has_text text="0.037661" /> 544 <has_text text="0.037661" />
422 </assert_contents>
423 </output>
424 </test>
425 <!-- test #6 - issue 6 -->
426 <test>
427 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
428 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
429 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
430 <param name="tesC" value="none"/>
431 <param name="facC" value="k._10"/>
432 <param name="labelFeatures" value="3"/>
433 <param name="fdr_features" value="ALL"/>
434 <param name="levCSV" value="k_3,k-4"/>
435 <param name="matchingC" value="none"/>
436 <output name="contrast_corcov">
437 <assert_contents>
438 <!-- column-labels line -->
439 <has_text text="featureID" />
440 <has_text text="factorLevel1" />
441 <has_text text="factorLevel2" />
442 <has_text text="correlation" />
443 <has_text text="covariance" />
444 <has_text text="vip4p" />
445 <has_text text="vip4o" />
446 <!-- first matched line -->
447 <has_text text="M349.2383T700" />
448 <has_text text="-0.1221966" />
449 <has_text text="-917311734" />
450 <has_text text="0.0304592" />
451 <has_text text="0.104748883" />
452 <has_text text="-0.002736415" />
453 <has_text text="-0.0113968" />
454 <has_text text="0.387723" />
455 <has_text text="-0.3812168081" />
456 <has_text text="0.154611878" />
457 </assert_contents>
458 </output>
459 </test>
460 <!-- test #7 - issue 8 -->
461 <test>
462 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
463 <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/>
464 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
465 <param name="tesC" value="none"/>
466 <param name="facC" value="k._10"/>
467 <param name="labelFeatures" value="3"/>
468 <param name="fdr_features" value="ALL"/>
469 <param name="levCSV" value="k_3,k-4"/>
470 <param name="matchingC" value="none"/>
471 <output name="contrast_corcov">
472 <assert_contents>
473 <!-- column-labels line -->
474 <has_text text="featureID" />
475 <has_text text="factorLevel1" />
476 <has_text text="factorLevel2" />
477 <has_text text="correlation" />
478 <has_text text="covariance" />
479 <has_text text="vip4p" />
480 <has_text text="vip4o" />
481 <!-- k1 rejected by levCSV, leaving only k_3 and k-4 -->
482 <not_has_text text="k1" />
483 <not_has_text text="other" />
484 <!-- first matched line -->
485 <has_text text="M200.005T296" />
486 <has_text text="-0.1829149760" />
487 <has_text text="-115723402" />
488 <has_text text="0.0892595" />
489 <has_text text="0.00492288" />
490 <has_text text="-0.00801895" />
491 <has_text text="0.0005356178" />
492 <has_text text="0.1848186" />
493 <has_text text="-0.428802311" />
494 <has_text text="0.0882045811" />
495 </assert_contents> 545 </assert_contents>
496 </output> 546 </output>
497 </test> 547 </test>
498 </tests> 548 </tests>
499 <help><![CDATA[ 549 <help><![CDATA[