Mercurial > repos > ethevenot > univariate

comparison univariate_config.xml @ 3:140290de7986 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 27bc6157f43574f038b3fb1be1f46ce4786e24b1
author ethevenot
date Sun, 30 Oct 2016 14:17:09 -0400
parents 09799fc16bc6
children 3017385625f6
comparison
equal deleted inserted replaced
2:09799fc16bc6 3:140290de7986
1 <tool id="Univariate" name="Univariate" version="2.1.4"> 1 <tool id="Univariate" name="Univariate" version="2.2.0">
2 <description>Univariate statistics</description> 2 <description>Univariate statistics</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.2.2">R</requirement> 5 <requirement type="package" version="3.2.2">R</requirement>
6 <requirement type="package">r-batch</requirement> 6 <requirement type="package">r-batch</requirement>
22 tesC "$tesC" 22 tesC "$tesC"
23 adjC "$adjC" 23 adjC "$adjC"
24 thrN "$thrN" 24 thrN "$thrN"
25 25
26 variableMetadata_out "$variableMetadata_out" 26 variableMetadata_out "$variableMetadata_out"
27 figure "$figure"
27 information "$information" 28 information "$information"
28 ]]></command> 29 ]]></command>
29 <inputs> 30 <inputs>
30 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> 31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
31 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> 32 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
52 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/> 53 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/>
53 </inputs> 54 </inputs>
54 55
55 <outputs> 56 <outputs>
56 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 57 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
58 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
57 <data name="information" label="${tool.name}_information.txt" format="txt"/> 59 <data name="information" label="${tool.name}_information.txt" format="txt"/>
58 </outputs> 60 </outputs>
59 61
60 <tests> 62 <tests>
61 <test> 63 <test>
62 <param name="dataMatrix_in" value="dataMatrix.tsv"/> 64 <param name="dataMatrix_in" value="dataMatrix.tsv"/>
63 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/> 65 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
64 <param name="variableMetadata_in" value="variableMetadata.tsv"/> 66 <param name="variableMetadata_in" value="variableMetadata.tsv"/>
65 <param name="facC" value="ageGroup"/> 67 <param name="facC" value="qual"/>
66 <param name="tesC" value="kruskal"/> 68 <param name="tesC" value="kruskal"/>
67 <param name="adjC" value="fdr"/> 69 <param name="adjC" value="fdr"/>
68 <param name="thrN" value="0.05"/> 70 <param name="thrN" value="0.05"/>
69 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/> 71 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
70 </test> 72 </test>
71 </tests> 73 </tests>
72 74
73 <help> 75 <help>
74 76
75 .. class:: infomark 77 .. class:: infomark
76 78
77 | **Tool update: See the 'NEWS' section at the bottom of the page** 79 | **Tool update: See the 'NEWS' section at the bottom of the page**
78 80
79 --------------------------------------------------- 81 ---------------------------------------------------
186 Output files 188 Output files
187 ------------ 189 ------------
188 190
189 variableMetadata_out.tabular 191 variableMetadata_out.tabular
190 | **variableMetadata** file identical to the file given as argument, except that (at least) three columns have been added: 192 | **variableMetadata** file identical to the file given as argument, except that (at least) three columns have been added:
191 | 1) [factor]_[test]_[class'a']-[class'b']_dif or [factor]_[test]_cor: difference of the means (ttest) or the medians (wilcoxon) between the two classes, or 'pearson' or 'spearman' correlations 193 | 1) [factor]_[test]_[class'a'].[class'b']_dif or [factor]_[test]_cor: difference of the means (ttest) or the medians (wilcoxon) between the two classes, or 'pearson' or 'spearman' correlations
192 | 2) [factor]_[test]_[class'a']-[class'b']_[method] or [factor]_[test]_[method]: adjusted p-values 194 | 2) [factor]_[test]_[class'a'].[class'b']_[method] or [factor]_[test]_[method]: adjusted p-values
193 | 3) [factor]_[test]_[class'a']-[class'b']_sig or [factor]_[test]_sig: significance (coded as '1' if below the threshold and '0' otherwise) 195 | 3) [factor]_[test]_[class'a'].[class'b']_sig or [factor]_[test]_sig: significance (coded as '1' if below the threshold and '0' otherwise)
194 | In the case of 'anova' and 'kruskal', the columns 2) and 3) appear first to give the results from the ANOVA or Kruskal Wallis test, and, when these tests are significant, the results of the pairwise comparisons are reported in additional columns (otherwise NA in these columns): in the case of ANOVA, the Tukey HSD post-hoc analysis is used (for each comparison, the difference between means, p value, and significance are provided); in the case of Kruskal Wallis, the Nemenyi is performed (PMCMR package) (for each pairwise comparison, the difference between medians, p value and significance are provided) 196 | In the case of 'anova' and 'kruskal', the columns 2) and 3) appear first to give the results from the ANOVA or Kruskal Wallis test, and then the results of the pairwise comparisons are reported in additional columns (otherwise NA in these columns): in the case of ANOVA, the Tukey HSD post-hoc analysis is used (for each comparison, the difference between means, p value, and significance are provided); in the case of Kruskal Wallis, the Nemenyi is performed (PMCMR package) (for each pairwise comparison, the difference between medians, p value and significance are provided); note that since version 2.2.0, the p-values of the post-hoc pairwise comparisons (ANOVA or Kruskal) are further corrected for multiple testing over all variables (as the p-value of the omnibus test in column 2)
195 | 197 |
196 198
199 figure.pdf
200 | File containing the graphics of all significant tests: boxplots (respectively scatterplots with the regression line in red and the R2 value) are displayed when the factor of interest is qualitative (respectively quantitative). The variable name and the corrected p-value is indicated in the title of each plot
201 |
202
197 information.txt 203 information.txt
198 | File with all messages and warnings generated during the computation 204 | File with all messages and warnings generated during the computation
199 | 205 |
200 206
201 --------------------------------------------------- 207 ---------------------------------------------------
212 218
213 ---- 219 ----
214 NEWS 220 NEWS
215 ---- 221 ----
216 222
223 CHANGES IN VERSION 2.2.0
224 ========================
225
226 MAJOR MODIFICATION
227
228 ANOVA and Kruskal-Wallis: The p-values of the post-hoc tests (i.e. from pairwise comparisons) are now further corrected for multiple testing over all variables (previously, only the p-value of the omnibus test was corrected over all variables)
229
230 MINOR MODIFICATION
231
232 All values in the 'dif', adjusted p-value, and 'sig' columns are now displayed (previously, the values were set to NA when the p-value of the omnibus test was not significant)
233
234 NEW FEATURE
235
236 Graphic: a single pdf file containing the graphics of all significant tests is now produced as '_figure.pdf' output: boxplots (respectively scatterplots with the regression line in red and the R2 value) are displayed when the factor of interest is qualitative (respectively quantitative). The corrected p-value is indicated in the title of each plot
237
238
217 CHANGES IN VERSION 2.1.4 239 CHANGES IN VERSION 2.1.4
218 ======================== 240 ========================
219 241
220 NEW FEATURE 242 NEW FEATURE
221 243
243 ======================== 265 ========================
244 266
245 NEW FEATURE 267 NEW FEATURE
246 268
247 (corrected) p-value threshold can be set to any value between 0 and 1 269 (corrected) p-value threshold can be set to any value between 0 and 1
248 270
249 271 </help>
250 </help> 272
251 273 <citations>
252 <citations> 274 <citation type="bibtex">@Manual{,
253 <citation type="bibtex">@Manual{, 275 title = {R: A Language and Environment for Statistical Computing},
254 title = {R: A Language and Environment for Statistical Computing}, 276 author = {{R Core Team}},
255 author = {{R Core Team}}, 277 organization = {R Foundation for Statistical Computing},
256 organization = {R Foundation for Statistical Computing}, 278 address = {Vienna, Austria},
257 address = {Vienna, Austria}, 279 year = {2016},
258 year = {2016}, 280 url = {https://www.R-project.org/},
259 url = {https://www.R-project.org/}, 281 }</citation>
260 }</citation> 282 <citation type="bibtex">@Article{Thevenot2015,
261 <citation type="bibtex">@Article{Thevenot2015, 283 Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses},
262 Title = {Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses}, 284 Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe},
263 Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe}, 285 Journal = {Journal of Proteome Research},
264 Journal = {Journal of Proteome Research}, 286 Year = {2015},
265 Year = {2015}, 287 Note = {PMID: 26088811},
266 Note = {PMID: 26088811}, 288 Number = {8},
267 Number = {8}, 289 Pages = {3322-3335},
268 Pages = {3322-3335}, 290 Volume = {14},
269 Volume = {14}, 291
270 292 Doi = {10.1021/acs.jproteome.5b00354},
271 Doi = {10.1021/acs.jproteome.5b00354}, 293 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
272 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354} 294 }</citation>
273 }</citation> 295 <citation type="doi">10.1093/bioinformatics/btu813</citation>
274 <citation type="doi">10.1093/bioinformatics/btu813</citation> 296 </citations>
275 </citations> 297
276
277
278
279 Input files
280 ===========
281
282 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
283 | **1) copy/paste the values below in three distinct .txt files**
284 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy / ABiMS page by choosing:**
285 | **a) File Format: 'tabular'**
286 | **b) Convert spaces to tabs: 'Yes'**
287 |
288
289 **dataMatrix file**::
290
291 dataMatrix HU_017 HU_021 HU_027 HU_032 HU_041 HU_048 HU_049 HU_050 HU_052 HU_059 HU_060 HU_066 HU_072 HU_077 HU_090 HU_109 HU_110 HU_125 HU_126 HU_131 HU_134 HU_149 HU_150 HU_173 HU_179 HU_180 HU_182 HU_202 HU_204 HU_209
292 HMDB01032 2569204.92420381 6222035.77434915 17070707.9912636 1258838.24348419 13039543.0754619 1909391.77026598 3495.09386434063 2293521.90928998 128503.275117713 81872.5276382213 8103557.56578035 149574887.036181 1544036.41049333 7103429.53933206 14138796.50382 4970265.57952158 263054.73056162 1671332.30008058 88433.1944958815 23602331.2894815 18648126.5206986 1554657.98756878 34152.3646391152 209372.71275317 33187733.370626 202438.591636003 13581070.0886437 354170.810678102 9120781.48986975 43419175.4051586
293 HMDB03072 3628416.30251025 65626.9834353751 112170.118946651 3261804.34422417 42228.2787747563 343254.201250707 1958217.69317664 11983270.0435677 5932111.41638028 5511385.83359531 9154521.47755199 2632133.21209418 9500411.14556502 6551644.51726592 7204319.80891836 1273412.04795188 3260583.81592376 8932005.5351622 8340827.52597275 9256460.69197759 11217839.169041 5919262.81433556 11790077.0657915 9567977.80797097 73717.5811684739 9991787.29074293 4208098.14739633 623970.649925847 10904221.2642849 2171793.93621067
294 HMDB00792 429568.609438384 3887629.50527037 1330692.11658995 1367446.73023821 844197.447472453 2948090.71886592 1614157.90566884 3740009.19379795 3292251.66531919 2310688.79492013 4404239.59008605 3043289.12780863 825736.467181043 2523241.91730649 6030501.02648005 474901.604069803 2885792.42617652 2955990.64049134 1917716.3427982 1767962.67737699 5926203.40397675 1639065.69474684 346810.763557826 1054776.22313737 2390258.27543894 1831346.37315857 1026696.36904362 7079792.50047866 4368341.01359769 3495986.87280275
295
296
297 **sampleMetadata file**::
298
299 sampleMetadata age ageGrp
300 HU_017 41 experienced
301 HU_021 34 junior
302 HU_027 37 experienced
303 HU_032 38 experienced
304 HU_041 28 junior
305 HU_048 39 experienced
306 HU_049 50 senior
307 HU_050 30 junior
308 HU_052 51 senior
309 HU_059 81 senior
310 HU_060 55 senior
311 HU_066 25 junior
312 HU_072 47 experienced
313 HU_077 27 junior
314 HU_090 46 experienced
315 HU_109 32 junior
316 HU_110 50 senior
317 HU_125 58 senior
318 HU_126 45 experienced
319 HU_131 42 experienced
320 HU_134 48 experienced
321 HU_149 35 experienced
322 HU_150 49 experienced
323 HU_173 55 senior
324 HU_179 33 junior
325 HU_180 53 senior
326 HU_182 43 experienced
327 HU_202 42 experienced
328 HU_204 31 junior
329 HU_209 17.5 junior
330
331
332 **variableMetadata file**::
333
334 variableMetadata name
335 HMDB01032 Dehydroepiandrosterone sulfate
336 HMDB03072 Quinic acid
337 HMDB00792 Sebacic acid
338
339
340 Parameters
341 ==========
342
343 **Factor of interest:** "ageGroup"
344
345 **Test:** "Kruskal-Wallis rank test (qualitative, > 2 levels)"
346
347 **Method for multiple testing correction:** "fdr"
348
349 **(Corrected) p-value significance threshold:** 0.05
350
351
352 Output files
353 ============
354
355 +------------------------------+------------+
356 | File | Format |
357 +==============================+============+
358 | 1) dataMatrix | tabular |
359 +------------------------------+------------+
360 | 2) sampleMetadata | tabular |
361 +------------------------------+------------+
362 | 3) variableMetadata | tabular |
363 +------------------------------+------------+
364 | 4) information | text |
365 +------------------------------+------------+
366
367
368 ---------------------------------------------------
369
370
371 </tool> 298 </tool>