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comparison qualitymetrics_config.xml @ 2:596320b84315 draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
author ethevenot
date Thu, 11 Jan 2018 12:52:08 -0500
parents 6d3b7b6573d8
children acdf51018708
comparison
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1:6d3b7b6573d8 2:596320b84315
1 <tool id="quality_metrics" name="Quality Metrics" version="2.2.6"> 1 <tool id="quality_metrics" name="Quality Metrics" version="2.2.8">
2 <description>Metrics and graphics to check the quality of the data</description> 2 <description>Metrics and graphics to check the quality of the data</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.3.1">R</requirement>
6 <requirement type="package">r-batch</requirement> 5 <requirement type="package">r-batch</requirement>
7 <requirement type="package">bioconductor-ropls</requirement> 6 <requirement type="package">bioconductor-ropls</requirement>
8 </requirements> 7 </requirements>
9 8
10 <stdio> 9 <stdio>
178 Variable metadata file 177 Variable metadata file
179 | contains variable information. 178 | contains variable information.
180 | 179 |
181 180
182 Note: 181 Note:
183 | Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org; the formats of the 3 tables can be further checked with the **Check Format** module 182 | **Required formats** for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org (http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf)
184 | 183 | The formats of the 3 tables can be further checked with the **Check Format** module
184 |
185
185 186
186 Coefficient of Variation 187 Coefficient of Variation
187 | If 'yes' (not default): variables are classed according to the Coefficient of Variation (CV) 188 | If 'yes' (not default): variables are classed according to the Coefficient of Variation (CV)
188 | i.e.: CV of pools (and CV of samples if needed) are calculated and compared to a defined threshold; 189 | i.e.: CV of pools (and CV of samples if needed) are calculated and compared to a defined threshold;
189 | then variables are classed with a 0/1 coding. 190 | then variables are classed with a 0/1 coding.
249 250
250 ---- 251 ----
251 NEWS 252 NEWS
252 ---- 253 ----
253 254
255 CHANGES IN VERSION 2.2.8
256 ========================
257
258 MINOR MODIFICATION
259
260 In the case of a distinct sample order between dataMatrix and sampleMetadata, the sample order from the dataMatrix is matched to sampleMetadata internally for the computations and graphics without modifying the order in the sampleMetadata output (a warning is generated in the information file); to get the re-ordered dataMatrix as output, please use the Check Format module
261
254 CHANGES IN VERSION 2.2.6 262 CHANGES IN VERSION 2.2.6
255 ======================== 263 ========================
264
256 MINOR MODIFICATION 265 MINOR MODIFICATION
257 266
258 Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value) 267 Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value)
259 268
260 CHANGES IN VERSION 2.2.4 269 CHANGES IN VERSION 2.2.4
289 Year = {1997}, 298 Year = {1997},
290 Number = {4}, 299 Number = {4},
291 Pages = {396-406}, 300 Pages = {396-406},
292 Volume = {29}, 301 Volume = {29},
293 }</citation> 302 }</citation>
303 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
294 <citation type="doi">10.1093/bioinformatics/btu813</citation> 304 <citation type="doi">10.1093/bioinformatics/btu813</citation>
295 </citations> 305 </citations>
296 306
297 <!--
298
299 Input files
300 ===========
301
302 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
303 | **1) copy/paste the values below in three distinct .txt files**
304 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy page by choosing:**
305 | **Convert spaces to tabs: 'Yes'**
306 |
307
308 **dataMatrix file**::
309
310 dataMatrix QC_4 sam_44 sam_18 sam_23 blk_3 sam_9 sam_22 QC_6 blk_4
311 met_031 5601185.9 4446133.4 4144765.4 3085899.9 NA 6748534.9 5819543.8 3256720.3 NA
312 met_032 4.07 4.08 4.11 4.1 NA 4.04 4.13 4.11 NA
313 met_033 1448205184 1456986135 993364802.3 1162711600 5569143.2 1043559922 1465003454 1052094028 5247494.3
314 met_034 4.11 4.21 4.18 4.1 4.09 4.1 4.14 4.11 4.08
315 met_035 3777580.7 2296751 1890711.7 1767424.6 6567.5 1906253.5 3043253.9 2856958.5 7940.8
316 met_036 4.12 4.21 4.26 4.1 4.11 4.22 4.27 4.12 4.2
317 met_037 4982658.7 3751181.8 4219033.2 2425759.9 NA 11978184.4 4306459.5 3352187 NA
318 met_038 4.45 4.38 4.4 4.4 NA 4.44 4.46 4.32 NA
319 met_039 6658087.7 3231434.7 2932986.5 4098788.3 NA 3691132.6 6108614.4 4541941.9 NA
320 met_040 4.49 4.56 4.48 4.5 NA 4.45 4.54 4.46 NA
321
322 **sampleMetadata file**::
323
324 sampleMetadata injectionOrder batch sampleType
325 QC_4 19 batch1 pool
326 sam_44 20 batch1 sample
327 sam_18 23 batch1 sample
328 sam_23 27 batch1 sample
329 blk_3 31 batch1 blank
330 sam_9 34 batch1 sample
331 sam_22 38 batch1 sample
332 QC_6 42 batch1 pool
333 blk_4 43 batch1 blank
334
335 **variableMetadata file**::
336
337 variableMetadata number
338 met_031 31
339 met_032 32
340 met_033 33
341 met_034 34
342 met_035 35
343 met_036 36
344 met_037 37
345 met_038 38
346 met_039 39
347 met_040 40
348
349 Figure output
350 =============
351
352 | You should obtain with this very simplified dataset the following figure:
353 |
354
355 .. image:: qualitymetrics_workingExampleImage.png
356 :width: 600
357
358 -->
359
360 </tool> 307 </tool>