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comparison profia_config.xml @ 2:3f8ae071bdda draft

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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author ethevenot
date Mon, 22 Jan 2018 11:32:41 -0500
parents 4753e64cf694
children de9d1270a9ae
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1:4753e64cf694 2:3f8ae071bdda
1 <tool id="profia" name="proFIA" version="3.0.4"> 1 <tool id="profia" name="proFIA" version="3.1.0">
2 <description>Preprocessing of FIA-HRMS data</description> 2 <description>Preprocessing of FIA-HRMS data</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package">r-batch</requirement> 5 <requirement type="package">r-batch</requirement>
6 <requirement type="package">r-FNN</requirement>
7 <requirement type="package">r-maxLik</requirement>
8 <requirement type="package">r-minpack.lm</requirement>
9 <requirement type="package">r-pracma</requirement>
10 <requirement type="package">bioconductor-xcms</requirement>
11 <requirement type="package">bioconductor-plasFIA</requirement>
12 <requirement type="package">bioconductor-proFIA</requirement> 6 <requirement type="package">bioconductor-proFIA</requirement>
13 </requirements> 7 </requirements>
14 8
15 <stdio> 9 <stdio>
16 <exit_code range="1:" level="fatal" /> 10 <exit_code range="1:" level="fatal" />
24 #elif $inputs.input == "zip_file": 18 #elif $inputs.input == "zip_file":
25 zipfile $inputs.zip_file 19 zipfile $inputs.zip_file
26 #end if 20 #end if
27 21
28 ppmN "$ppmN" 22 ppmN "$ppmN"
23 dmzN "$dmzN"
29 ppmGroupN "$ppmGroupN" 24 ppmGroupN "$ppmGroupN"
25 dmzGroupN "$dmzGroupN"
30 fracGroupN "$fracGroupN" 26 fracGroupN "$fracGroupN"
31 kI "$kI" 27 imputeC "$imputeC"
28
29 #if $advCpt.opcC == "full"
30 bandCoverageN "$advCpt.bandCoverageN"
31 sizeMinN "$advCpt.sizeMinN"
32 scanMinI "$advCpt.scanMinI"
33 scanMaxI "$advCpt.scanMaxI"
34 #end if
32 35
33 dataMatrix_out "$dataMatrix_out" 36 dataMatrix_out "$dataMatrix_out"
34 sampleMetadata_out "$sampleMetadata_out" 37 sampleMetadata_out "$sampleMetadata_out"
35 variableMetadata_out "$variableMetadata_out" 38 variableMetadata_out "$variableMetadata_out"
36 figure "$figure" 39 figure "$figure"
51 <validator type="empty_field"/> 54 <validator type="empty_field"/>
52 </param> 55 </param>
53 </when> 56 </when>
54 </conditional> 57 </conditional>
55 58
56 <param name="ppmN" label="Maximum deviation between centroids during band detection (in ppm)" type="text" value = "5" help="[ppm]" /> 59 <param name="ppmN" label="Maximum deviation between centroids during band detection (in ppm)" type="text" value = "7" help="[ppm]" />
57 <param name="ppmGroupN" label="Accuracy of the mass spectrometer to be used during feature alignment (in ppm)" type="text" value = "5" help="[ppmGroup] Should be inferior or equal to the deviation parameter above." /> 60 <param name="dmzN" label="Minimal maximum deviation between centroids during band detection (in Da)" type="text" value = "0.001" help="[dmz] shloud be at most 0.002 for high resolution" />
61 <param name="ppmGroupN" label="Accuracy of the mass spectrometer to be used during feature alignment (in ppm)" type="text" value = "3" help="[ppmGroup] Should be inferior to the ppm parameter above." />
62 <param name="dmzGroupN" label="Minimal accuracy of the mass spectrometer to be used during feature alignment (in Da)" type="text" value = "0.0005" help="[dmzGroup] shloud be at most 0.002 for high resolution" />
58 <param name="fracGroupN" label=" Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment" type="text" value = "0.5" help="[fracGroup]" /> 63 <param name="fracGroupN" label=" Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment" type="text" value = "0.5" help="[fracGroup]" />
59 <param name="kI" label="Number of neighbour features to be used for imputation (select 0 to skip the imputation step)" type="text" value = "5" help="[k]" /> 64 <param name="imputeC" label="Imputation method" type="select" help="[imputation]">
65 <option value="None">None</option>
66 <option value="randomForest" selected="true">randomForest</option>
67 </param>
68
69
70
71 <conditional name="advCpt">
72 <param name="opcC" type="select" label="Advanced parameters" >
73 <option value="default" selected="true">Use default</option>
74 <option value="full">Full parameter list</option>
75 </param>
76 <when value="default"/>
77 <when value="full">
78 <param name="bandCoverageN" type="float" value="0.3" label="Minimum fraction of centroids in the estimated injection window for a band to be built" help="[bandCoverage] Must be between 0 and 1"/>
79 <param name="sizeMinN" type="text" value="none" label="Minimum number of consecutive centroids for a band to be built" help="[sizeMin] If set to 'none', the half of the estimated injection window will be used"/>
80 <param name="scanMinI" type="integer" value="1" label="First scan to be preprocessed" help="[scanMin]"/>
81 <param name="scanMaxI" type="text" value="none" label="Last scan to be preprocessed" help="[scanMax] Set to 'none' to preprocess up to the last acquired scan"/>
82 </when>
83 </conditional>
84
85
86
60 </inputs> 87 </inputs>
61 88
62 <outputs> 89 <outputs>
63 <data name="dataMatrix_out" label="${tool.name}_dataMatrix.tsv" format="tabular" ></data> 90 <data name="dataMatrix_out" label="${tool.name}_dataMatrix.tsv" format="tabular" ></data>
64 <data name="sampleMetadata_out" label="${tool.name}_sampleMetadata.tsv" format="tabular" ></data> 91 <data name="sampleMetadata_out" label="${tool.name}_sampleMetadata.tsv" format="tabular" ></data>
70 <tests> 97 <tests>
71 <test> 98 <test>
72 <param name="inputs|input" value="zip_file" /> 99 <param name="inputs|input" value="zip_file" />
73 <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" /> 100 <param name="inputs|zip_file" value="input-plasFIA.zip" ftype="zip" />
74 <param name="ppmN" value="2"/> 101 <param name="ppmN" value="2"/>
102 <param name="dmzN" value="0.0005"/>
75 <param name="ppmGroupN" value="1"/> 103 <param name="ppmGroupN" value="1"/>
104 <param name="dmzGroupN" value="0.0005"/>
76 <param name="fracGroupN" value="0.1"/> 105 <param name="fracGroupN" value="0.1"/>
77 <param name="kI" value="2"/> 106 <param name="imputeC" value="randomForest"/>
78 <output name="dataMatrix_out" file="output-dataMatrix.tsv" /> 107 <output name="dataMatrix_out" file="output-dataMatrix.tsv" />
79 <output name="information"> 108 <output name="information">
80 <assert_contents> 109 <assert_contents>
81 <has_text text="722 groups have been done" /> 110 <has_text text="707 groups have been done" />
82 <has_text text="3 samples x 644 variables" /> 111 <has_text text="3 samples x 707 variables" />
83 <has_text text="78 excluded variables (near zero variance)" /> 112 <has_text text="2089 peaks detected" />
84 <has_text text="2101 peaks detected" />
85 </assert_contents> 113 </assert_contents>
86 </output> 114 </output>
87 </test> 115 </test>
88 </tests> 116 </tests>
89 117
90 <help> 118 <help>
91 119
92 .. class:: infomark 120 .. class:: infomark
93 121
94 **Author** Alexis Delabriere and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr) 122 **Author** Alexis Delabriere and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)
95 123
97 125
98 .. class:: infomark 126 .. class:: infomark
99 127
100 **Please cite** 128 **Please cite**
101 129
102 Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. 130 Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. (2017). *proFIA*: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, **33**:3767-3775. `https://doi.org/10.1093/bioinformatics/btx458 &lt;https://doi.org/10.1093/bioinformatics/btx458&gt;`_
103 131
104 --------------------------------------------------- 132 ---------------------------------------------------
105 133
106 .. class:: infomark 134 .. class:: infomark
107 135
139 167
140 .. class:: infomark 168 .. class:: infomark
141 169
142 **References** 170 **References**
143 171
144 | Delabriere A., Hohenester U., Junot C. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. 172 | Delabriere A., Hohenester U., Junot C. and Thevenot E.A. (2017). proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, **33**:3767-3775. (https://doi.org/10.1093/bioinformatics/btx458)
145 | Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. (http://dx.doi.org/10.1007/s11306-012-0449-x) 173 | Draper J., Lloyd A., Goodacre R. and Beckmann M. (2013). Flow infusion electrospray ionisation mass spectrometry for high throughput, non-targeted metabolite fingerprinting: a review. *Metabolomics* 9, 4-29. (https://doi.org/10.1007/s11306-012-0449-x)
146 | Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. (http://dx.doi.org/10.1021/ac201267k) 174 | Fuhrer T., Dominik H., Boris B. and Zamboni N. (2011). High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry. *Analytical Chemistry* 83, 7074-7080. (https://doi.org/10.1021/ac201267k)
147 | Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. (http://dx.doi.org/10.1021/ac7024915) 175 | Madalinski G., Godat E., Alves S., Lesage D., Genin E., Levi P., Labarre J., Tabet J., Ezan E. and Junot, C. (2008). Direct introduction of biological samples into a LTQ-orbitrap hybrid mass spectrometer as a tool for fast metabolome analysis. *Analytical Chemistry* 80, 3291-3303. (https://doi.org/10.1021/ac7024915)
148 176
149 --------------------------------------------------- 177 ---------------------------------------------------
150 178
151 ----------------- 179 -----------------
152 Workflow position 180 Workflow position
214 242
215 ---------- 243 ----------
216 Parameters 244 Parameters
217 ---------- 245 ----------
218 246
219 Maximum deviation between centroids during band detection; in ppm (default = 5) 247 Maximum deviation between centroids during band detection; in ppm (default = 7)
220 | m/z tolerance of centroids corresponding to the same ion from one scan to the other. 248 | m/z tolerance of centroids corresponding to the same ion from one scan to the other.
221 | 249 |
222 250
223 Accuracy of the mass spectrometer to be used during feature alignment; in ppm (default = 5) 251 Minimal maximum deviation between centroids during band detection; in Da (default = 0.001); to avoid bias at low mass values, the deviation is the maximum between this quantity and the deviation in ppm
224 | Should be inferior or equal to the deviation parameter above. 252 | minimum m/z tolerance of centroids corresponding to the same ion from one scan to the other.
253 |
254
255 Accuracy of the mass spectrometer to be used during feature alignment; in ppm (default = 3); should be less than the ppm parameter used for detection
256 | Should be inferior or equal to the ppm deviation parameter above.
225 | 257 |
226 258
259 Minimal accuracy of the mass spectrometer to be used during feature alignment; in Da (default = 0.0005); to avoid bias at low mass values; the deviation is the maximum between this quantity and the deviation in ppm
260 |
261
227 Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment (default = 0.5) 262 Minimum fraction of samples in which a peak should be detected in at least one class to be kept during feature alignment (default = 0.5)
228 | Identical to the corresponding parameter in XCMS. 263 | Identical to the corresponding parameter in XCMS.
229 | 264 |
230 265
231 Number of neighbour features to be used for imputation (default = 5) 266 Imputation method for missing values (default = 'randomForest')
232 | Select 0 to skip the imputation step. 267 |
233 | 268
234 269 Minimum fraction of centroids in the estimated injection window for a band to be built (advanced; default = 0.3)
270 |
271
272 Minimum number of consecutive centroids for a band to be built (advanced; default = half of the size of the estimated injection window)
273 |
274
275 First scan to be preprocessed (advanced; default = 1)
276 |
277
278 Last scan to be preprocessed (advanced; default = last acquisition scan)
279 |
235 280
236 ------------ 281 ------------
237 Output files 282 Output files
238 ------------ 283 ------------
239 284
273 318
274 ---- 319 ----
275 NEWS 320 NEWS
276 ---- 321 ----
277 322
323 CHANGES IN VERSION 3.1.0
324 ========================
325
326 NEW FEATURE
327
328 randomForest method implemented for imputation of missing values
329
330 CHANGES IN VERSION 3.0.6
331 ========================
332
333 NEW FEATURE
334
335 dmz (and dmzGroup) parameters added for the peak detection and grouping steps; bandCoverage, sizeMin, scanMin, and scanMax added as advanced parameters for peak detection
336
337
278 CHANGES IN VERSION 3.0.4 338 CHANGES IN VERSION 3.0.4
279 ======================== 339 ========================
280 340
281 MINOR MODIFICATION 341 MINOR MODIFICATION
282 342
298 Creation of the tool 358 Creation of the tool
299 359
300 </help> 360 </help>
301 361
302 <citations> 362 <citations>
303 <citation type="bibtex">@Article{DelabriereSubmitted, 363 <citation type="doi">10.1093/bioinformatics/btx458</citation>
304 Title = {proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry},
305 Author = {Delabriere, Alexis and Hohenester, Ulli and Colsch, Benoit and Junot, Christophe and Fenaille, Francois and Thevenot, Etienne A},
306 Journal = {submitted},
307 Year = {submitted},
308 Pages = {--},
309 Volume = {},
310 Doi = {}
311 }</citation>
312 <citation type="doi">10.1093/bioinformatics/btu813</citation> 364 <citation type="doi">10.1093/bioinformatics/btu813</citation>
313 </citations> 365 </citations>
314 366
315 </tool> 367 </tool>