Mercurial > repos > marie-tremblay-metatoul > normalization
comparison NmrNormalization_xml.xml @ 5:3d00a98974b7 draft
planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
author | lecorguille |
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date | Tue, 02 Oct 2018 12:14:47 -0400 |
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children | 221cbd549c40 |
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1 <tool id="normalization" name="Normalization" version="1.0.6"> | |
2 | |
3 <description> Normalization of (preprocessed) spectra </description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="1.1_4">r-batch</requirement> | |
7 </requirements> | |
8 | |
9 <stdio> | |
10 <exit_code range="1:" level="fatal" /> | |
11 </stdio> | |
12 | |
13 <command><![CDATA[ | |
14 Rscript $__tool_directory__/NmrNormalization_wrapper.R | |
15 | |
16 ## Data matrix of bucketed and integrated spectra | |
17 dataMatrix $dataMatrix | |
18 | |
19 ## Normalization method | |
20 scalingMethod $scalingMethod.method | |
21 #if $scalingMethod.method == "PQN": | |
22 ## Sample metadata matrix | |
23 sampleMetadata $scalingMethod.sampleMetadata | |
24 | |
25 ## Biological factor of interest (column number in samplemetadata) | |
26 factor $scalingMethod.factor | |
27 | |
28 ## Reference class | |
29 controlGroup $scalingMethod.controlGroup | |
30 #end if | |
31 #if $scalingMethod.method == "QuantitativeVariable": | |
32 ## Sample metadata matrix | |
33 sampleMetadata $scalingMethod.sampleMetadata | |
34 | |
35 ## Biological factor of interest (column number in samplemetadata) | |
36 factor $scalingMethod.factor | |
37 #end if | |
38 | |
39 ## Spectra representation | |
40 graphType $graphType | |
41 | |
42 ## Outputs | |
43 logOut $logOut | |
44 dataMatrixOut $dataMatrixOut | |
45 graphOut $graphOut | |
46 ]]></command> | |
47 | |
48 <inputs> | |
49 <param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" /> | |
50 | |
51 <conditional name="scalingMethod" > | |
52 <param name="method" label="Normalization method" type="select" help="Default method is total intensity" > | |
53 <option value="None">None normalization</option> | |
54 <option value="Total">Total intensity</option> | |
55 <option value="PQN">Probabilistic Quotient Normalization</option> | |
56 <option value="QuantitativeVariable">Quantitative variable</option> | |
57 </param> | |
58 <when value="None" /> | |
59 <when value="Total" /> | |
60 <when value="PQN"> | |
61 <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" /> | |
62 <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" /> | |
63 <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/> | |
64 </when> | |
65 <when value="QuantitativeVariable"> | |
66 <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" /> | |
67 <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" /> | |
68 </when> | |
69 </conditional> | |
70 | |
71 <param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation"> | |
72 <option value="None"> none </option> | |
73 <option value="Overlay"> Overlay </option> | |
74 <option value="One_per_individual"> One_per_individual </option> | |
75 </param> | |
76 </inputs> | |
77 | |
78 | |
79 <outputs> | |
80 <data format="txt" name="logOut" label="${tool.name}_log" /> | |
81 <data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" /> | |
82 <data format="pdf" name="graphOut" label="${tool.name}_spectra" > | |
83 <filter> graphType != "None" </filter> | |
84 </data> | |
85 </outputs> | |
86 | |
87 <tests> | |
88 <test> | |
89 <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" /> | |
90 <conditional name="scalingMethod" > | |
91 <param name="method" value="Total" /> | |
92 </conditional> | |
93 <param name="graphType" value="Overlay" /> | |
94 <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" /> | |
95 </test> | |
96 </tests> | |
97 | |
98 <help> | |
99 | |
100 .. class:: infomark | |
101 | |
102 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr) | |
103 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en) | |
104 | |
105 --------------------------------------------------- | |
106 | |
107 .. class:: infomark | |
108 | |
109 **Please cite** | |
110 | |
111 F. Dieterle, A. Ross, G. Schlotterbeck, and H. Senn (2006). Probabilistic Quotient Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures. Application in 1H NMR Metabonomics. | |
112 Analytical Chemistry 78(13): 4281-4290. | |
113 | |
114 --------------------------------------------------- | |
115 | |
116 =============== | |
117 Normalization | |
118 =============== | |
119 | |
120 ----------- | |
121 Description | |
122 ----------- | |
123 | |
124 Normalization (operation applied on each (preprocessed) individual spectrum) of preprocessed data | |
125 | |
126 ----------------- | |
127 Workflow position | |
128 ----------------- | |
129 | |
130 **Upstream tools** | |
131 | |
132 +----------------------+------------------------------------+---------+-------------+ | |
133 | Name | output file | format | parameter | | |
134 +======================+====================================+=========+=============+ | |
135 | NMR_Bucketing | Normalization_bucketedData.tsv | tabular | Ions Matrix | | |
136 +----------------------+------------------------------------+---------+-------------+ | |
137 | |
138 | |
139 | |
140 | |
141 **Downstream tools** | |
142 | |
143 +---------------------------+----------------------+--------+ | |
144 | Name | Output file | Format | | |
145 +===========================+======================+========+ | |
146 |Univariate | variableMetadata.tsv | Tabular| | |
147 +---------------------------+----------------------+--------+ | |
148 |Multivariate | sampleMetadata.tsv | Tabular| | |
149 +---------------------------+----------------------+--------+ | |
150 | | variableMetadata.tsv | Tabular| | |
151 +---------------------------+----------------------+--------+ | |
152 | |
153 | |
154 ----------- | |
155 Input files | |
156 ----------- | |
157 | |
158 +---------------------------+------------+ | |
159 | Parameter : num + label | Format | | |
160 +===========================+============+ | |
161 | DataMatrix | Tabular | | |
162 +---------------------------+------------+ | |
163 | |
164 **DataMAtrix** | |
165 | |
166 | variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values | |
167 | |
168 | |
169 ---------- | |
170 Parameters | |
171 ---------- | |
172 | |
173 DataMatrix | |
174 | see "Input files" section above | |
175 | | |
176 | |
177 Normalization method | |
178 | normalization to apply on each spectrum: | |
179 | |
180 +---------------------------+--------------------------------------+ | |
181 | Name | Normalization | | |
182 +===========================+======================================+ | |
183 |None | No | | |
184 +---------------------------+--------------------------------------+ | |
185 |Total | Total intensity | | |
186 +---------------------------+--------------------------------------+ | |
187 |PQN | Probabilistic Quotient Normalization | | |
188 +---------------------------+--------------------------------------+ | |
189 |QuantitativeVariable | Weight, osmolality, ... | | |
190 +---------------------------+--------------------------------------+ | |
191 | |
192 | |
193 sampleMetadata | |
194 | sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values | |
195 | Mandatory for "PQN" or "Quantitative" normalization method | |
196 | The row names must be identical to the column names of the dataMatrix file | |
197 | | |
198 | |
199 | |
200 Spectra representation: | |
201 | Graphical chart of bucketed and integrated raw files | |
202 | If "Overlay": the n (sample number) spectra are overlaid on the same figure | |
203 | If "One_per_individual": pdf file includes n pages (1 per sample) | |
204 | | |
205 | |
206 | |
207 ------------ | |
208 Output files | |
209 ------------ | |
210 | |
211 | |
212 dataMatrix.tsv | |
213 | tabular output | |
214 | Data matrix with p rows (variable) and n columns (samples) containing the intensities | |
215 | | |
216 | |
217 spectra.pdf | |
218 | pdf output | |
219 | Graphical chart of bucketed and integrated data | |
220 | | |
221 | |
222 | |
223 --------------------------------------------------- | |
224 | |
225 --------------- | |
226 Working example | |
227 --------------- | |
228 | |
229 | |
230 .. class:: warningmark | |
231 | |
232 Under construction | |
233 | |
234 .. image:: ./static/images/Mth_Travaux.png | |
235 :width: 100 | |
236 | |
237 | |
238 --------------------------------------------------- | |
239 | |
240 -------------- | |
241 Changelog/News | |
242 -------------- | |
243 | |
244 **Version 1.0.3 - 30/01/2017** | |
245 | |
246 - BUGFIX: Fix a bug: stack overflow for integers | |
247 | |
248 **Version 1.0.2 - 22/10/2016** | |
249 | |
250 - NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data | |
251 | |
252 **Version 1.0.1 - 14/04/2016** | |
253 | |
254 - TEST: refactoring to pass planemo test using conda dependencies | |
255 | |
256 **Version 2015-01-28 - 28/01/2015** | |
257 | |
258 </help> | |
259 <citations> | |
260 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
261 </citations> | |
262 </tool> |