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date Mon, 23 Dec 2019 09:26:20 -0500
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1 <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0">
2
3 <description> Annotation of complex mixture bidimensional NMR spectra </description>
4
5 <stdio>
6 <exit_code range="1:" level="fatal" />
7 </stdio>
8
9 <command>
10 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
11 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
12
13
14 ## XLS file
15 xlsfile $zip_xlsfile
16
17 ## 2D-NMR sequences to annotate
18 cosy_2dsequences $cosy_2dsequences
19 jres_2dsequences $jres_2dsequences
20 hmbc_2dsequences $hmbc_2dsequences
21 hsqc_2dsequences $hsqc_2dsequences
22 tocsy_2dsequences $tocsy_2dsequences
23
24 ## In-house databases
25 inHouse_DB_choices.choice ${inHouse_DB_choices.choice}
26 #if str($inHouse_DB_choices.choice) == 'yes':
27 inHouse_DB_cosy.choice ${inHouse_DB_cosy.choice}
28 #if str($inHouse_DB_cosy.choice) == 'yes':
29 cosyDB $cosyDB
30 #end if
31 inHouse_DB_hmbc.choice ${inHouse_DB_hmbc.choice}
32 #if str($inHouse_DB_hmbc.choice) == 'yes':
33 hmbcDB $hmbcDB
34 #end if
35 inHouse_DB_hsqc.choice ${inHouse_DB_hsqc.choice}
36 #if str($inHouse_DB_hsqc.choice) == 'yes':
37 hsqcDB $hsqcDB
38 #end if
39 inHouse_DB_jres.choice ${inHouse_DB_jres.choice}
40 #if str($inHouse_DB_jres.choice) == 'yes':
41 jresDB $jresDB
42 #end if
43 inHouse_DB_tocsy.choice ${inHouse_DB_tocsy.choice}
44 #if str($inHouse_DB_tocsy.choice) == 'yes':
45 tocsyDB $tocsyDB
46 #end if
47 #end if
48
49 ## Tolerances
50 tolppm1 $tolppm1
51 tolppm2 $tolppm2
52 tolppmJRES $tolppmJRES
53
54
55 ## Treshold (probability score)
56 threshold $threshold
57
58 ## Unicity
59 unicity $unicity
60
61 ## Outputs
62 logOut $logOut
63 annotationCOSY $annotationCOSY
64 ppmCommunCOSY $ppmCommunCOSY
65 annotationJRES $annotationJRES
66 ppmCommunJRES $ppmCommunJRES
67 annotationHMBC $annotationHMBC
68 ppmCommunHMBC $ppmCommunHMBC
69 annotationHSQC $annotationHSQC
70 ppmCommunHSQC $ppmCommunHSQC
71 annotationTOCSY $annotationTOCSY
72 ppmCommunTOCSY $ppmCommunTOCSY
73 annotationCombination $annotationCombination
74 AnnotationGraph $AnnotationGraph
75
76 </command>
77
78 <inputs>
79 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
80
81 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence">
82 <option value="yes" > yes </option>
83 <option value="no" selected="true"> no </option>
84 </param>
85 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
86 <option value="yes" > yes </option>
87 <option value="no" selected="true"> no </option>
88 </param>
89 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence">
90 <option value="yes" > yes </option>
91 <option value="no" selected="true"> no </option>
92 </param>
93 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence">
94 <option value="yes" > yes </option>
95 <option value="no" selected="true"> no </option>
96 </param>
97 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence">
98 <option value="yes" > yes </option>
99 <option value="no" selected="true"> no </option>
100 </param>
101
102 <conditional name="inHouse_DB_choices">
103 <param name="choice" type="select" label="In-house database" help="Choose if you want to use use in-house database to annotate" >
104 <option value="yes" > yes </option>
105 <option value="no" selected="true"> no </option>
106 </param>
107 <when value="yes">
108 <conditional name="inHouse_DB_cosy">
109 <param name="choice" type="select" label="COSY In-house database" help="Choose if you want to use use in-house database to annotate COSY sequence" >
110 <option value="yes" > yes </option>
111 <option value="no" selected="true"> no </option>
112 </param>
113 <when value="yes">
114 <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" />
115 </when>
116 </conditional>
117 <conditional name="inHouse_DB_hmbc">
118 <param name="choice" type="select" label="HMBC In-house database" help="Choose if you want to use use in-house database to annotate HMBC sequence" >
119 <option value="yes" > yes </option>
120 <option value="no" selected="true"> no </option>
121 </param>
122 <when value="yes">
123 <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" />
124 </when>
125 </conditional> <conditional name="inHouse_DB_hsqc">
126 <param name="choice" type="select" label="HSQC In-house database" help="Choose if you want to use use in-house database to annotate HSQC sequence" >
127 <option value="yes" > yes </option>
128 <option value="no" selected="true"> no </option>
129 </param>
130 <when value="yes">
131 <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" />
132 </when>
133 </conditional> <conditional name="inHouse_DB_jres">
134 <param name="choice" type="select" label="JRES In-house database" help="Choose if you want to use use in-house database to annotate JRES sequence" >
135 <option value="yes" > yes </option>
136 <option value="no" selected="true"> no </option>
137 </param>
138 <when value="yes">
139 <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" />
140 </when>
141 </conditional>
142 <conditional name="inHouse_DB_tocsy">
143 <param name="choice" type="select" label="TOCSY In-house database" help="Choose if you want to use use in-house database to annotate TOCSY sequence" >
144 <option value="yes" > yes </option>
145 <option value="no" selected="true"> no </option>
146 </param>
147 <when value="yes">
148 <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" />
149 </when>
150 </conditional>
151 </when>
152 <when value="no" />
153 </conditional>
154
155 <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" />
156 <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" />
157 <param name="tolppmJRES" type="float" value="0.002" help="Tolerance on chemical shift for the y-axis for the JRES sequence. Default value is 0.002 (Hz)" />
158
159 <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" />
160
161 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="">
162 <option value="no">No</option>
163 <option value="yes"></option>
164 </param>
165
166 </inputs>
167
168 <outputs>
169 <data format="txt" name="logOut" label="${tool.name}_log" />
170 <data format="tabular" name="annotationCOSY" label="annotationCosy" >
171 <filter> cosy_2dsequences != "no" </filter>
172 </data>
173 <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" >
174 <filter> cosy_2dsequences != "no" </filter>
175 </data>
176
177 <data format="tabular" name="annotationJRES" label="annotationJres" >
178 <filter> jres_2dsequences != "no" </filter>
179 </data>
180 <data format="tabular" name="ppmCommunJRES" label="duplicateJres" >
181 <filter> jres_2dsequences != "no" </filter>
182 </data>
183
184 <data format="tabular" name="annotationHMBC" label="annotationHmbc" >
185 <filter> hmbc_2dsequences != "no" </filter>
186 </data>
187 <data format="tabular" name="ppmCommunHMBC" label="duplicateHmbc" >
188 <filter> hmbc_2dsequences != "no" </filter>
189 </data>
190
191 <data format="tabular" name="annotationHSQC" label="annotationHsqc" >
192 <filter> hsqc_2dsequences != "no" </filter>
193 </data>
194 <data format="tabular" name="ppmCommunHSQC" label="duplicateHsqc" >
195 <filter> hsqc_2dsequences != "no" </filter>
196 </data>
197
198 <data format="tabular" name="annotationTOCSY" label="annotationTocsy" >
199 <filter> tocsy_2dsequences != "no" </filter>
200 </data>
201 <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" >
202 <filter> tocsy_2dsequences != "no" </filter>
203 </data>
204
205 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
206 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
207 </outputs>
208
209 <help>
210
211 .. class:: infomark
212
213 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
214
215 .. class:: infomark
216
217
218 ---------------------------------------------------
219
220 ============================
221 Bidimensional NMR Annotation
222 ============================
223
224 -----------
225 Description
226 -----------
227
228 BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
229
230 -----------------
231 Workflow position
232 -----------------
233
234 **Upstream tools**
235
236 ========================= ================= ======= =========
237 Name output file format parameter
238 ========================= ================= ======= =========
239 NA NA NA NA
240 ========================= ================= ======= =========
241
242
243 **Downstream tools**
244
245 ========================= ================= ======= =========
246 Name output file format parameter
247 ========================= ================= ======= =========
248 NA NA NA NA
249 ========================= ================= ======= =========
250
251
252
253 -----------
254 Input files
255 -----------
256
257 +---------------------------+------------+
258 | Parameter : num + label | Format |
259 +===========================+============+
260 | 1 : Choose your inputs | xlsx |
261 +---------------------------+------------+
262
263 **Choose your inputs**
264 | xlsx file can include several peak lists, coming from several 2D NMR sequences
265 |
266
267 .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png
268
269 ----------
270 Parameters
271 ----------
272
273 Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s)
274 | COSY: yes/no
275 | JRES: yes/no
276 | HMBC: yes/no
277 | HSQC: yes/no
278 | TOCSY: yes/no
279 | Default value is no
280 |
281
282 In-house databases
283 | Use of your own databases to annotate peak list(s)
284 | If YES: parameters **COSY In-house database**, **JRES In-house database**, ** HMBC In-house database**, **HSQC In-house database** and **TOCSY In-house database** are visible
285 | Select one or more in-house database
286 |
287
288
289 Tolerances
290 | tolppm1: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the x-axis
291 | tolppm2: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the y-axis
292 | tolppmJRES: Maximum variation of the chemical shift (due to experimental conditions) of a peak for the JRES sequence
293 | Default values: 0.01 and 0.01 ppm; 0.002 Hz
294 |
295
296
297 Threshold
298 | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
299 | Default value: 0
300 |
301
302
303 Unicity of annotation
304 | All the peaks assigned to more than one metabolite are removed
305 |
306
307
308 ------------
309 Output files
310 ------------
311 COSY
312 | tabular outputs
313 | annotationCOSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
314 | ppmCommunCOSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
315 | Only display if COSY was chosen
316 |
317
318
319 JRES
320 | tabular outputs
321 | annotationJRES: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
322 | ppmCommunJRES: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
323 | Only display if JRES was chosen
324 |
325
326
327 HMBC
328 | tabular outputs
329 | annotationHMBC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
330 | ppmCommunHMBC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
331 | Only display if HMBC was chosen
332 |
333
334
335 HSQC
336 | tabular outputs
337 | annotationHSQC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
338 | ppmCommunHSQC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
339 | Only display if HSQC was chosen
340 |
341
342
343 TOCSY
344 | tabular outputs
345 | annotationTOCSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
346 | ppmCommunTOCSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
347 | Only display if TOCSY was chosen
348 |
349
350
351 annotationCombination
352 | tabular outputs
353 | Array with p rows (corresponding to the identified metabolites) including the Metabolite name, the COSY presence probability, the JRES presence probability, the HMBC presence probability, the HSQC presence probability, the TOCSY presence probability and the averageScore
354 | Depends on the chosen sequences
355 | Only display if 2 or more sequences have be chosen
356
357
358 AnnotationGraph.pdf
359 | pdf output
360 | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
361
362
363
364 ---------------------------------------------------
365
366 -------
367 Example
368 -------
369 Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
370
371 .. image:: ./static/images/OutputsExampleMix.png
372 :width: 500
373
374 </help>
375
376 </tool>