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comparison nmr_bucketing/NmrBucketing_xml.xml @ 2:3cd762aac7a4 draft

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author marie-tremblay-metatoul
date Thu, 20 Apr 2017 08:53:46 -0400
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1 <tool id="NmrBucketing" name="NMR_Bucketing" version="1.0.3">
2
3 <description> Bucketing and integration of NMR Bruker raw data</description>
4
5 <requirements>
6 <requirement type="package" version="1.1_4">r-batch</requirement>
7 <requirement type="package" version="1.8.8">r-pracma</requirement>
8 </requirements>
9
10 <stdio>
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13
14 <command>
15 Rscript '$__tool_directory__/NmrBucketing_wrapper.R'
16
17 #if $inputs.input == "tsv_file":
18 tsvfile '$inputs.tsv_file'
19 #elif $inputs.input == "zip_file":
20 zipfile '$inputs.zip_file'
21 #end if
22
23
24 ## Bucket width
25 bucket_width $bucket_width
26
27 ## Spectra borders
28 left_border $left_border
29 right_border $right_border
30
31
32 ## Spectra representation
33 graphType $graphType
34
35 ## Exclusion zone
36 zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
37 #if str($zone_exclusion_choices.choice) == 'yes':
38 #for $i in $zone_exclusion_choices.conditions:
39 zone_exclusion_left ${i.zone_exclusion_left}
40 zone_exclusion_right ${i.zone_exclusion_right}
41 #end for
42 #end if
43
44 ## Outputs
45 logOut log.log
46 dataMatrixOut '$dataMatrixOut'
47 sampleOut '$sampleOut'
48 variableOut '$variableOut'
49 graphOut '$graphOut'; cat log.log
50 </command>
51
52 <inputs>
53 <conditional name="inputs">
54 <param name="input" type="select" label="Choose your inputs method" >
55 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
56 <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>
57 </param>
58 <when value="zip_file">
59 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
60 </when>
61 <when value="tsv_file">
62 <param name="tsv_file" type="data" format="tabular" label="Tsv file" />
63 </when>
64 </conditional>
65
66 <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>
67
68 <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>
69 <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>
70
71 <conditional name="zone_exclusion_choices">
72 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
73 <option value="yes" > yes </option>
74 <option value="no" selected="true"> no </option>
75 </param>
76 <when value="yes">
77 <repeat name="conditions" title="exclusion zones">
78 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
79 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
80 </repeat>
81 </when>
82 <when value="no">
83 </when>
84 </conditional>
85
86 <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">
87 <option value="None"> none </option>
88 <option value="Overlay"> Overlay </option>
89 <option value="One_per_individual"> One_per_individual </option>
90 </param>
91
92 </inputs>
93
94 <outputs>
95 <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" />
96 <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" />
97 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
98 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
99 <filter> graphType != "None" </filter>
100 </data>
101 </outputs>
102
103 <tests>
104 <test>
105 <param name="inputs|input" value="zip_file" />
106 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" />
107 <param name="bucket_width" value="0.01" ftype="zip" />
108 <param name="left_border" value="9.3" />
109 <param name="right_border" value="0.8" />
110 <param name="zone_exclusion_choices|choice" value="yes" />
111 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_left" value="6.0" />
112 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_right" value="4.24" />
113 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_left" value="3.99" />
114 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_right" value="3.19" />
115 <param name="graphType" value="Overlay" />
116 <output name="dataMatrixOut" file="MTBLS1_bucketedData.tabular" />
117 <output name="sampleOut" file="MTBLS1_sampleMetadata.tabular" />
118 <output name="variableOut" file="MTBLS1_variableMetadata.tabular" />
119 </test>
120 </tests>
121
122 <help>
123
124 .. class:: infomark
125
126 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr), Marion Landi (marion.landi@clermont.inra.fr) and Franck Giacomoni (fgiacomoni@clermont.inra.fr)
127
128
129 =============
130 NMR Bucketing
131 =============
132
133 -----------
134 Description
135 -----------
136
137 Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data
138
139 -----------------
140 Workflow position
141 -----------------
142
143 **Upstream tools**
144
145 ========================= ============================ =======
146 Name output file format
147 ========================= ============================ =======
148 NMRAlignment NMR_Alignment_alignedSpectra tsv
149 ========================= ============================ =======
150
151 **Downstream tools**
152
153 +---------------------------+----------------------+--------+
154 | Name | Output file | Format |
155 +===========================+======================+========+
156 |NmrNormalization | dataMatrix.tsv | Tabular|
157 +---------------------------+----------------------+--------+
158 |Univariate | variableMetadata.tsv | Tabular|
159 +---------------------------+----------------------+--------+
160 |Multivariate | sampleMetadata.tsv | Tabular|
161 +---------------------------+----------------------+--------+
162 | | variableMetadata.tsv | Tabular|
163 +---------------------------+----------------------+--------+
164
165
166 -----------
167 Input files
168 -----------
169
170 +---------------------------+------------+
171 | Parameter : num + label | Format |
172 +===========================+============+
173 | 1 : Choose your inputs | zip |
174 +---------------------------+------------+
175 | 1 : Choose your inputs | tsv |
176 +---------------------------+------------+
177
178 **Choose your inputs**
179
180 You have three methods for your inputs:
181
182 | Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories).
183 | Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows).
184
185 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
186 :width: 800
187
188 ----------
189 Parameters
190 ----------
191
192 Bucket width
193 | size of windows
194 |
195
196 Left limit
197 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm
198 |
199
200 Right limit
201 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm
202 |
203
204 Exclusion zone(s)
205 | Spectral regions to exclude, water, solvents, ... resonance
206 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
207 | If NO: no zone to exclude
208 | Default value is NO
209 |
210
211 Left exclusion zone
212 | Upper boundary of exclusion zone
213 |
214
215 Right exclusion zone
216 | Lower boundary of exclusion zone
217
218 | *Notes:*
219 | - these parameters can be used several times using the "Add new exclusion zones" button
220 |
221
222 Spectra representation:
223 | Graphical chart of bucketed and integrated raw files
224 | If "Overlay": the n (sample number) spectra are overlaid on the same figure
225 | If "One_per_individual": pdf file includes n pages (1 per sample)
226 |
227
228
229 ------------
230 Output files
231 ------------
232
233
234 bucketedData.tsv
235 | tabular output
236 | Data matrix with p rows (buckets) and n columns (samples) containing the intensities
237 |
238
239 sampleMetadata.tsv
240 | tabular output
241 | 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.
242 |
243
244 variableMetadata.tsv
245 | tabular output
246 | 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.
247 |
248
249 spectra.pdf
250 | pdf output
251 | Graphical chart of bucketed and integrated data
252 |
253
254
255 ---------------------------------------------------
256
257 ---------------
258 Working example
259 ---------------
260
261
262 .. class:: warningmark
263
264 Under construction
265
266 .. image:: ./static/images/Mth_Travaux.png
267 :width: 100
268
269 ---------------------------------------------------
270
271 Changelog/News
272 --------------
273
274 **Version 1.0.3 - 24/10/2016**
275
276 - ENHANCEMENT: add possibility of bucketing processed files (upstream tools)
277
278 **Version 1.0.2 - 12/08/2016**
279
280 - ENHANCEMENT: x-axis customization: add chemical shift labels
281
282 **Version 1.0.1 - 04/04/2016**
283
284 - TEST: refactoring to pass planemo test using conda dependencies
285
286
287 **Version 2015-01-08 - 08/01/2015**
288
289 </help>
290 <citations>
291 <citation type="doi">10.1093/bioinformatics/btu813</citation>
292 </citations>
293 </tool>