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comparison univariate_config.xml @ 2:09799fc16bc6 draft

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planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe
author ethevenot
date Sat, 06 Aug 2016 12:42:42 -0400
parents fdefbc780d2e
children 140290de7986
comparison
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1:fdefbc780d2e 2:09799fc16bc6
1 <tool id="Univariate" name="Univariate" version="2.1.2"> 1 <tool id="Univariate" name="Univariate" version="2.1.4">
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>
7 <requirement type="package">r-pmcmr</requirement> 7 <requirement type="package">r-PMCMR</requirement>
8 </requirements> 8 </requirements>
9 9
10 <stdio>
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13
10 <command><![CDATA[ 14 <command><![CDATA[
11 $__tool_directory__/univariate_wrapper.R 15 Rscript $__tool_directory__/univariate_wrapper.R
12 dataMatrix_in "$dataMatrix_in" 16
13 sampleMetadata_in "$sampleMetadata_in" 17 dataMatrix_in "$dataMatrix_in"
14 variableMetadata_in "$variableMetadata_in" 18 sampleMetadata_in "$sampleMetadata_in"
15 19 variableMetadata_in "$variableMetadata_in"
16 facC "$facC" 20
17 tesC "$tesC" 21 facC "$facC"
18 adjC "$adjC" 22 tesC "$tesC"
19 thrN "$thrN" 23 adjC "$adjC"
20 24 thrN "$thrN"
21 variableMetadata_out "$variableMetadata_out" 25
22 information "$information" 26 variableMetadata_out "$variableMetadata_out"
27 information "$information"
23 ]]></command> 28 ]]></command>
24
25 <inputs> 29 <inputs>
26 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> 30 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
27 <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" /> 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" />
28 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> 32 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
29 <param name="facC" label="Factor of interest" type="text" help="Name of the column of the sample metadata table corresponding to the qualitative or quantitative variable"/> 33 <param name="facC" label="Factor of interest" type="text" help="Name of the column of the sample metadata table corresponding to the qualitative or quantitative variable"/>
30 <param name="tesC" label="Test" type="select" help=""> 34 <param name="tesC" label="Test" type="select" help="">
31 <option value="ttest">ttest (qualitative, 2 levels)</option> 35 <option value="ttest">ttest (qualitative, 2 levels)</option>
32 <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option> 36 <option value="wilcoxon">Wilcoxon test (qualitative, 2 levels)</option>
33 <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option> 37 <option value="anova">Analysis of variance (qualitative, more than 2 levels)</option>
34 <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option> 38 <option value="kruskal">Kruskal-Wallis rank test (qualitative, more than 2 levels)</option>
35 <option value="pearson">Pearson correlation test (quantitative)</option> 39 <option value="pearson">Pearson correlation test (quantitative)</option>
36 <option value="spearman">Spearman correlation rank test (quantitative)</option> 40 <option value="spearman">Spearman correlation rank test (quantitative)</option>
37 </param> 41 </param>
38 <param name="adjC" label="Method for multiple testing correction" type="select" help=""> 42 <param name="adjC" label="Method for multiple testing correction" type="select" help="">
39 <option value="fdr">fdr</option> 43 <option value="fdr">fdr</option>
40 <option value="BH">BH</option> 44 <option value="BH">BH</option>
41 <option value="bonferroni">bonferroni</option> 45 <option value="bonferroni">bonferroni</option>
42 <option value="BY">BY</option> 46 <option value="BY">BY</option>
43 <option value="hochberg">hochberg</option> 47 <option value="hochberg">hochberg</option>
44 <option value="holm">holm</option> 48 <option value="holm">holm</option>
45 <option value="hommel">hommel</option> 49 <option value="hommel">hommel</option>
46 <option value="none">none</option> 50 <option value="none">none</option>
47 </param> 51 </param>
48 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/> 52 <param name="thrN" type="float" value="0.05" label="(Corrected) p-value significance threshold" help="Must be between 0 and 1"/>
49 </inputs> 53 </inputs>
50 54
51 <outputs> 55 <outputs>
52 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 56 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
53 <data name="information" label="${tool.name}_information.txt" format="txt"/> 57 <data name="information" label="${tool.name}_information.txt" format="txt"/>
54 </outputs> 58 </outputs>
55 59
56 <tests> 60 <tests>
57 <test> 61 <test>
58 <param name="dataMatrix_in" value="dataMatrix.tsv"/> 62 <param name="dataMatrix_in" value="dataMatrix.tsv"/>
59 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/> 63 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
60 <param name="variableMetadata_in" value="variableMetadata.tsv"/> 64 <param name="variableMetadata_in" value="variableMetadata.tsv"/>
61 <param name="facC" value="ageGroup"/> 65 <param name="facC" value="ageGroup"/>
62 <param name="tesC" value="kruskal"/> 66 <param name="tesC" value="kruskal"/>
63 <param name="adjC" value="fdr"/> 67 <param name="adjC" value="fdr"/>
64 <param name="thrN" value="0.05"/> 68 <param name="thrN" value="0.05"/>
65 <output name="variableMetadata_out" file="variableMetadata-output.tsv"/> 69 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
66 </test> 70 </test>
67 </tests> 71 </tests>
68 72
69 <help> 73 <help>
70 74
71 .. class:: infomark 75 .. class:: infomark
72 76
73 | **Tool update: See the 'NEWS' section at the bottom of the page** 77 | **Tool update: See the 'NEWS' section at the bottom of the page**
197 --------------------------------------------------- 201 ---------------------------------------------------
198 202
199 --------------- 203 ---------------
200 Working example 204 Working example
201 --------------- 205 ---------------
206
207 .. class:: infomark
208
209 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
210
211 ---------------------------------------------------
212
213 ----
214 NEWS
215 ----
216
217 CHANGES IN VERSION 2.1.4
218 ========================
219
220 NEW FEATURE
221
222 Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)
223
224 INTERNAL MODIFICATIONS
225
226 Minor internal changes for toolshed export
227
228 CHANGES IN VERSION 2.1.2
229 ========================
230
231 INTERNAL MODIFICATIONS
232
233 Minor internal changes for toolshed export
234
235 CHANGES IN VERSION 2.1.1
236 ========================
237
238 INTERNAL MODIFICATIONS
239
240 Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples)
241
242 CHANGES IN VERSION 2.0.1
243 ========================
244
245 NEW FEATURE
246
247 (corrected) p-value threshold can be set to any value between 0 and 1
248
249
250 </help>
251
252 <citations>
253 <citation type="bibtex">@Manual{,
254 title = {R: A Language and Environment for Statistical Computing},
255 author = {{R Core Team}},
256 organization = {R Foundation for Statistical Computing},
257 address = {Vienna, Austria},
258 year = {2016},
259 url = {https://www.R-project.org/},
260 }</citation>
261 <citation type="bibtex">@Article{Thevenot2015,
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},
263 Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe},
264 Journal = {Journal of Proteome Research},
265 Year = {2015},
266 Note = {PMID: 26088811},
267 Number = {8},
268 Pages = {3322-3335},
269 Volume = {14},
270
271 Doi = {10.1021/acs.jproteome.5b00354},
272 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
273 }</citation>
274 <citation type="doi">10.1093/bioinformatics/btu813</citation>
275 </citations>
276
277
202 278
203 Input files 279 Input files
204 =========== 280 ===========
205 281
206 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:** 282 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
289 +------------------------------+------------+ 365 +------------------------------+------------+
290 366
291 367
292 --------------------------------------------------- 368 ---------------------------------------------------
293 369
294 ----
295 NEWS
296 ----
297
298 CHANGES IN VERSION 2.1.2
299 ========================
300
301 Minor internal changes for toolshed export
302
303 CHANGES IN VERSION 2.1.1
304 ========================
305
306 Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples)
307
308 CHANGES IN VERSION 2.0.1
309 ========================
310
311 (corrected) p-value threshold can be set to any value between 0 and 1
312
313
314 </help>
315
316 <citations/>
317 370
318 </tool> 371 </tool>