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comparison NmrBucketing_xml.xml @ 0:a99a6026c972 draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 44fd4fc42930d2e9ad7b77cf575f2231547de15c
author marie-tremblay-metatoul
date Fri, 08 Apr 2016 10:56:14 -0400
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1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.1">
2
3 <description> Bucketing and integration of NMR Bruker raw data</description>
4
5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="package" version="1.1_4">r-batch</requirement>
8 <requirement type="package" version="1.8.8">r-pracma</requirement>
9 </requirements>
10
11 <stdio>
12 <exit_code range="1:" level="fatal" />
13 </stdio>
14
15 <command>
16 Rscript $__tool_directory__/NmrBucketing_wrapper.R
17
18 #if $inputs.input == "lib":
19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
20 #elif $inputs.input == "zip_file":
21 zipfile $inputs.zip_file
22 #end if
23
24
25 ## Bucket width
26 bucket_width $bucket_width
27
28 ## Spectra borders
29 left_border $left_border
30 right_border $right_border
31
32
33 ## Spectra representation
34 graphType $graphType
35
36 ## Exclusion zone
37 zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
38 #if str($zone_exclusion_choices.choice) == 'yes':
39 #for $i in $zone_exclusion_choices.conditions:
40 zone_exclusion_left ${i.zone_exclusion_left}
41 zone_exclusion_right ${i.zone_exclusion_right}
42 #end for
43 #end if
44
45 ## Outputs
46 logOut log.log
47 dataMatrixOut $dataMatrixOut
48 sampleOut $sampleOut
49 variableOut $variableOut
50 graphOut $graphOut; cat log.log
51 </command>
52
53 <inputs>
54 <conditional name="inputs">
55 <param name="input" type="select" label="Choose your inputs method" >
56 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
57 <option value="lib" >Library directory name</option>
58 </param>
59 <when value="zip_file">
60 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
61 </when>
62 <when value="lib">
63 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
64 <validator type="empty_field"/>
65 </param>
66 </when>
67
68 </conditional>
69
70 <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>
71
72 <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>
73 <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>
74
75 <conditional name="zone_exclusion_choices">
76 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
77 <option value="yes" > yes </option>
78 <option value="no" selected="true"> no </option>
79 </param>
80 <when value="yes">
81 <repeat name="conditions" title="exclusion zones">
82 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
83 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
84 </repeat>
85 </when>
86 <when value="no">
87 </when>
88 </conditional>
89
90 <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">
91 <option value="None"> none </option>
92 <option value="Overlay"> Overlay </option>
93 <option value="One_per_individual"> One_per_individual </option>
94 </param>
95
96 </inputs>
97
98 <outputs>
99 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
100 <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" />
101 <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" />
102 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
103 <filter> graphType != "None" </filter>
104 </data>
105 </outputs>
106
107
108 <tests>
109 <test>
110 <param name="inputs|input" value="zip_file" />
111 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" />
112 <param name="bucket_width" value="0.01" ftype="zip" />
113 <param name="left_border" value="9.3" />
114 <param name="right_border" value="0.8" />
115 <param name="zone_exclusion_choices|choice" value="yes" />
116 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_left" value="6.0" />
117 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_right" value="4.24" />
118 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_left" value="3.99" />
119 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_right" value="3.19" />
120 <param name="graphType" value="Overlay" />
121 <output name="dataMatrixOut" file="MTBLS1_bucketedData.tabular" />
122 <output name="sampleOut" file="MTBLS1_sampleMetadata.tabular" />
123 <output name="variableOut" file="MTBLS1_variableMetadata.tabular" />
124 </test>
125 </tests>
126
127 <help>
128
129 .. class:: infomark
130
131 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr), Marion Landi (marion.landi@clermont.inra.fr) and Franck Giacomoni (fgiacomoni@clermont.inra.fr)
132
133
134 =============
135 NMR Bucketing
136 =============
137
138 -----------
139 Description
140 -----------
141
142 Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data
143
144 -----------------
145 Workflow position
146 -----------------
147
148 **Upstream tools**
149
150 ========================= ================= ======= =========
151 Name output file format parameter
152 ========================= ================= ======= =========
153 NA NA zip NA
154 ========================= ================= ======= =========
155
156
157 **Downstream tools**
158
159 +---------------------------+----------------------+--------+
160 | Name | Output file | Format |
161 +===========================+======================+========+
162 |NmrNormalization | dataMatrix.tsv | Tabular|
163 +---------------------------+----------------------+--------+
164 |Univariate | variableMetadata.tsv | Tabular|
165 +---------------------------+----------------------+--------+
166 |Multivariate | sampleMetadata.tsv | Tabular|
167 +---------------------------+----------------------+--------+
168 | | variableMetadata.tsv | Tabular|
169 +---------------------------+----------------------+--------+
170
171
172 -----------
173 Input files
174 -----------
175
176 +---------------------------+------------+
177 | Parameter : num + label | Format |
178 +===========================+============+
179 | 1 : Choose your inputs | zip |
180 +---------------------------+------------+
181
182 **Choose your inputs**
183
184 You have two methods for your inputs:
185
186 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
187 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
188
189 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
190 :width: 800
191
192 ----------
193 Parameters
194 ----------
195
196 Bucket width
197 | size of windows
198 |
199
200 Left limit
201 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm
202 |
203
204 Right limit
205 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm
206 |
207
208 Exclusion zone(s)
209 | Spectral regions to exclude, water, solvents, ... resonance
210 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
211 | If NO: no zone to exclude
212 | Default value is NO
213 |
214
215 Left exclusion zone
216 | Upper boundary of exclusion zone
217 |
218
219 Right exclusion zone
220 | Lower boundary of exclusion zone
221
222 | *Notes:*
223 | - these parameters can be used several times using the "Add new exclusion zones" button
224 |
225
226 Spectra representation:
227 | Graphical chart of bucketed and integrated raw files
228 | If "Overlay": the n (sample number) spectra are overlaid on the same figure
229 | If "One_per_individual": pdf file includes n pages (1 per sample)
230 |
231
232
233 ------------
234 Output files
235 ------------
236
237
238 bucketedData.tsv
239 | tabular output
240 | Data matrix with p rows (buckets) and n columns (samples) containing the intensities
241 |
242
243 sampleMetadata.tsv
244 | tabular output
245 | file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order: the rownames of sampleMetadata must be identical to the colnames of the bucketedData. Can add columns with numeric and/or character sample metadata. This file is optional in the normalization step and mandatory in the statistical analysis step of the workflow.
246 |
247
248 variableMetadata.tsv
249 | tabular output
250 | file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order: the rownames of variableMetadata must be identical to the rownames of the bucketedData. Can add columns with numeric and/or character variable metadata. This file is mandatory in the statistical analysis step of the workflow.
251 |
252
253 spectra.pdf
254 | pdf output
255 | Graphical chart of bucketed and integrated data
256 |
257
258
259 ---------------------------------------------------
260
261 ---------------
262 Working example
263 ---------------
264
265
266 .. class:: warningmark
267
268 Under construction
269
270 .. image:: ./static/images/Mth_Travaux.png
271 :width: 100
272
273
274 </help>
275 <citations>
276 <citation type="doi">10.1093/bioinformatics/btu813</citation>
277 </citations>
278 </tool>
279