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planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde
author ethevenot
date Thu, 04 Aug 2016 11:40:35 -0400
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1 <tool id="Determine_BC" name="Determine_batch_correction" version="2.0.0">
2 <description>to choose between linear, lowess and loess methods</description>
3
4 <requirements>
5 <requirement type="package" version="3.3.1">R</requirement>
6 <requirement type="package">r-batch</requirement>
7 <requirement type="package">r-ade4</requirement>
8 <requirement type="package">r-pcaMethods</requirement>
9 </requirements>
10
11 <stdio>
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14
15 <command><![CDATA[
16 Rscript $__tool_directory__/batch_correction_wrapper.R
17 analyse "determine_bc"
18 sampleMetadata "$sampleMetadata"
19 dataMatrix "$dataMatrix"
20 ref_factor "$ref_factor"
21 #if str($advance.option ) == 'show':
22 span $advance.span
23 #else:
24 span "none"
25 #end if
26 out_graph_pdf "$out_graph_pdf"
27 out_preNormSummary "$out_preNormSummary"
28 ]]></command>
29
30 <inputs>
31 <param name="dataMatrix" type="data" label="Data Matrix file " help="" format="tabular" />
32 <param name="sampleMetadata" type="data" label="Sample metadata file " help="must contain at least the three following columns: 'batch' + 'injectionOrder' + 'sampleType'" format="tabular" />
33 <param name="ref_factor" type="text" label="Factor of interest " help="column name of the factor of interest (often a biological factor); if none, leave 'batch'" value="batch" />
34 <conditional name="advance">
35 <param name="option" type="select" label="Advanced options" help="should only be put at 'show' if you have good understanding of the span parameter and are willing to adjust it">
36 <option value="show">show</option>
37 <option value="hide" selected="true">hide</option>
38 </param>
39 <when value="hide">
40 <param name="span" type="hidden" value="none"/>
41 </when>
42 <when value="show">
43 <param name="span" type="float" value="0.85" label="span" help="applied to lowess and loess regression"/>
44 </when>
45 </conditional>
46 </inputs>
47
48 <outputs>
49 <data name="out_graph_pdf" label="Determine_BC_graph" format="pdf" ></data>
50 <data name="out_preNormSummary" label="Determine_BC_preNormSummary" format="tabular" ></data>
51 </outputs>
52
53 <tests>
54 <test>
55 <param name="dataMatrix" value="input-determinebc-dataMatrix.tsv"/>
56 <param name="sampleMetadata" value="input-determinebc-sampleMetadata.tsv"/>
57 <param name="ref_factor" value="batch"/>
58 <param name="option" value="hide"/>
59 <param name="span" value="none"/>
60 <output name="out_preNormSummary" file="output-determinebc-preNormSummary.txt"/>
61 </test>
62 </tests>
63
64 <help>
65
66 .. class:: infomark
67
68 **Authors** Franck Giacomoni and Marion Landi (for interface and wrapper) and Jean-Francois Martin and Melanie Petera (for R)
69
70 ---------------------------------------------------
71
72 .. class:: infomark
73
74 **Please cite** If you use this tool, please cite `F.M. van der Kloet, I. Bobeldijk, E.R. Verheij, R.H. Jellema. (2009). "Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping." Journal of Proteome Research p5132-5141 &lt;http://www.ncbi.nlm.nih.gov/pubmed/19754161&gt;`_
75
76 ---------------------------------------------------
77
78 ==========================
79 Determine_batch_correction
80 ==========================
81
82 -----------
83 Description
84 -----------
85
86 | Allows to choose between linear or non-linear (lowess or loess) functions for batch correction
87 | using quality control pooled samples (QC-pools) with correction algorithm as mentioned by Van Der Kloet (J Prot Res 2009).
88 |
89 | Warning : this module does *not* deliver which choice should be made in model type;
90 | it only provides tools to help users to determine which choice may be appropriate, based on their own expertise.
91 |
92 | This tool is meant to be used prior to the Batch_correction tool to help make a choice in parameters,
93 | but it is not a requirement and thus can be avoided.
94
95
96 -----------------
97 Workflow position
98 -----------------
99
100 .. image:: ./static/images/metabolomics/determine_batch_correction.png
101 :width: 800
102
103
104 -----------
105 Input files
106 -----------
107
108 +--------------------------+-----------+
109 | Parameter : num + label | Format |
110 +==========================+===========+
111 | 1 : Data Matrix file | tabular |
112 +--------------------------+-----------+
113 | 2 : Sample metadata file | tabular |
114 +--------------------------+-----------+
115
116
117 Data Matrix file must contain the intensity values of the variables.
118 | First line must contain all the samples' names
119 | First column must contain all the variables' ID
120 |
121
122 Sample metadata file must contain at least the three following columns:
123 | "batch" to identify the batches of analyses
124 | "injectionOrder" (integers) defining the injection order of all samples (QC-pools as well as analysed samples)
125 | "sampleType" indicating if a sample ("sample") or a QC-pool ("pool"); each batch needs
126 | at least 3 QC-pools for intra-batch linear adjustment and 8 for lo(w)ess adjustment
127
128
129 .. class:: warningmark
130
131 NO MISSING DATA are allowed
132
133
134 ----------
135 Parameters
136 ----------
137
138 Factor of interest
139 | name of the factor (column header) that will be used as a categorical variable for plots.
140 | (often a biological factor ; if none, leave “batch”).
141 | This factor does not affect correction calculation.
142 |
143
144 Advanced options
145 | should only be put at "show" if you have good understanding of the span parameter and are willing to adjust it.
146 |
147
148 Span
149 | - when advanced option is at "hide" (default)
150 | default is 1 for loess regression and is two times the ratio between number of pools and number of samples for lowess regression.
151 | - when advanced option is at "show" :
152 | filled value is used for lowess and loess regression.
153
154
155 ------------
156 Output files
157 ------------
158
159 Determine_BC_preNormSummary.tabular
160 | tabular output
161 | Meaning of results of diagnosis analysis
162 | 0 : no preliminary-condition problem
163 | 1 : standard deviation of QC-pools or samples = 0
164 | 2 : insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess)
165 | 3 : significant difference between QC-pools and samples means
166 | 4 : denominator =0 when on 1 pool per batch non-0
167 | 5 : (linear regression only) the slopes ratio “QC-pools/samples” is lower than -0.2
168 |
169
170 Determine_BC_graph.pdf
171 | graphical output
172 | One page per ion. Plots regression curves for all methods allowed and plot.design results regarding the factor of interest.
173
174
175 ---------------------------------------------------
176
177 ---------------
178 Working example
179 ---------------
180
181
182 .. class:: warningmark
183
184 Soon see the corresponding "Page"
185
186
187 </help>
188
189 <citations>
190 <citation type="bibtex">@Article{Kloet2009,
191 Title = {Analytical error reduction using single point calibration for accurate and precise metabolomic phenotyping},
192 Author = {van der Kloet, Frans M. and Bobeldijk, Ivana and Verheij, Elwin R. and Jellema, Renger H.},
193 Journal = {Journal of Proteome Research},
194 Year = {2009},
195 Note = {PMID: 19754161},
196 Number = {11},
197 Pages = {5132-5141},
198 Volume = {8},
199
200 Doi = {10.1021/pr900499r},
201 Url = {http://pubs.acs.org/doi/abs/10.1021/pr900499r}
202 }</citation>
203 <citation type="doi">10.1093/bioinformatics/btu813</citation>
204 </citations>
205
206 <!--
207 Input files
208 ===========
209
210 | **These two input files can be used in the purview "URL/Text:" of the tool "Get Data/Upload File",**
211 | **by checking the box "Convert spaces to tabs: YES"**
212
213 Metadata_samples.txt
214 Model input Sample metadata file::
215
216 samples idLIMS serie factor01 factor02 batch injectionOrder sampleType
217 POOL1 POOL1 pool p pool 01_08_2011 1 p
218 X12588 12588 3 validation 2 01_08_2011 2 s
219 X17736 17736 3 Q1 1 01_08_2011 3 s
220 X15432 15432 3 validation 1 01_08_2011 4 s
221 X17159 17159 3 Q4 1 01_08_2011 5 s
222 X14325 14325 3 validation 2 01_08_2011 6 s
223 X17419 17419 3 Q4 1 01_08_2011 7 s
224 X16437 16437 3 Q4 1 01_08_2011 8 s
225 X16172 16172 3 Q4 2 01_08_2011 9 s
226 X16392 16392 3 Q4 2 01_08_2011 10 s
227 X13875 13875 3 validation 2 01_08_2011 11 s
228 POOL2 POOL2 pool p pool 01_08_2011 12 p
229 X13117 13117 3 Q4 2 01_08_2011 13 s
230 X13341 13341 3 Q1 2 01_08_2011 14 s
231 X16888 16888 3 Q4 1 01_08_2011 15 s
232 X17489 17489 3 Q4 2 01_08_2011 16 s
233 X12718 12718 3 Q1 2 01_08_2011 17 s
234 X16235 16235 3 Q4 2 01_08_2011 18 s
235 X16878 16878 3 Q1 1 01_08_2011 19 s
236 X12701 12701 3 validation 1 01_08_2011 20 s
237 X16220 16220 3 Q4 2 01_08_2011 21 s
238 X15635 15635 3 Q4 1 01_08_2011 22 s
239
240
241 Intensity_matrix.txt
242 Model input Matrix Ions file BEFORE IMPLEMENTATION::
243
244 samples POOL1 X12588 X17736 X15432 X17159 X14325 X17419 X16437 X16172 X16392 X13875 POOL2 X13117 X13341 X16888 X17489 X12718 X16235 X16878 X12701 X16220 X15635
245 ion01 188.4140625 219.729126 122.5697632 123.5487671 805.8852539 183.4683838 37.33084106 151.8625488 97.12005615 91.24694824 69.87762451 195.4349365 112.4111938 136.7092285 159.9987793 172.1585693 0 117.5420532 133.6679688 80.05419922 160.0006104 760.0488281
246 ion02 82.02575684 87.11358643 79.82391357 80.33862305 83.08575439 94.27703857 76.02288818 77.04394531 76.97564697 84.17669678 81.04943848 86.44024658 84.11865234 83.71282959 77.75219727 79.15936279 75.98492432 78.2835083 78.98760986 73.98388672 72.20550537 82.16448975
247 ion03 25.31900024 24.2960968 23.29342651 31.54063416 30.3830719 22.42404175 35.44485474 26.38783264 17.1401825 21.27339172 20.25959778 26.33859253 18.17146301 26.32852173 24.30648804 28.34313965 29.37016296 18.23519897 24.48402405 25.38140869 24.35777283 21.31071472
248 ion04 65.87536621 62.68716431 46.60232544 62.77856445 29.53218079 47.59136963 90.13983154 28.35336304 58.74325562 31.39331055 23.32928467 30.39666748 41.43960571 21.27049255 88.1161499 29.36820984 24.30200195 25.00007629 45.60662842 103.293457 37.46994019 87.09295654
249 ion05 0 103.728544 279.5808214 884.2333448 824.5072072 434.6439081 764.82768 799.0972595 398.4002569 382.5370891 74.55342827 0 636.6596277 514.3863309 741.690017 412.3166491 660.8996555 57.36593795 102.2085264 455.6403091 548.6145486 515.8412195
250 ion06 2711.785156 3465.292969 2469.75 3435.259766 2482.3125 2593.654297 1407.915039 1291.253906 2241.734375 1444.189453 3363.683594 2578.642578 2633.181641 3397.763672 3706.855469 3647.212891 3548.410156 3714.640625 1889.213867 2262.707031 2107.417969 2763.21875
251 ion07 164.9023438 192.40625 140.7609863 192.4053955 139.7540283 140.748291 84.60144043 86.1819458 150.762207 89.90411377 207.5949707 164.0512695 149.8706055 186.336792 214.6140137 202.5360107 214.6877441 195.4482422 117.4679565 127.2941895 142.78479 163.0666504
252
253
254 Parameters
255 ==========
256
257 Factor analysis -> **batch**
258
259
260 Output files
261 ============
262
263 out_preNormSummary.tabular:
264
265 ====== ============== ==============
266 labion batch.1.linear batch.1.lowess
267 ====== ============== ==============
268 ion01 2 2
269 ion02 2 2
270 ion03 2 2
271 ion04 2 2
272 ion05 1 1
273 ... ... ...
274 ====== ============== ==============
275
276
277 out_graph_pdf.pdf
278
279 .. image:: ./static/images/metabolomics/pdf_plotsituation.png
280 :width: 800
281 -->
282
283 </tool>