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comparison annotationRmn2D_xml.xml @ 2:dff7bde22102 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b3abcb650e9b38458aa0ac5f7d838811d982ff65"
author workflow4metabolomics
date Tue, 04 Feb 2020 10:59:26 -0500
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1:a4d2b1926e13 2:dff7bde22102
1 <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0">
2
3 <description> Annotation of complex mixture bidimensional NMR spectra </description>
4
5 <requirements>
6 <requirement type="package" version="1.1_5">r-batch</requirement>
7 <requirement type="package" version="0.8.3">r-dplyr</requirement>
8 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
9 <requirement type="package" version="4.0.17">r-openxlsx</requirement>
10 <requirement type="package" version="1.4.0">r-stringr</requirement>
11 <requirement type="package" version="1.0.2">r-tidyr</requirement>
12 </requirements>
13
14 <stdio>
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
18 <command>
19 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
20 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
21
22
23 ## XLS file
24 xlsfile '$zip_xlsfile'
25
26 ## 2D-NMR sequences to annotate
27 cosy_2dsequences $cosy_2dsequences
28 jres_2dsequences $jres_2dsequences
29 hmbc_2dsequences $hmbc_2dsequences
30 hsqc_2dsequences $hsqc_2dsequences
31 tocsy_2dsequences $tocsy_2dsequences
32
33 ## In-house databases
34 inHouse_DB_choices.choice ${inHouse_DB_choices.choice}
35 #if str($inHouse_DB_choices.choice) == 'yes':
36 inHouse_DB_cosy.choice ${inHouse_DB_choices.inHouse_DB_cosy.choice}
37 #if str($inHouse_DB_choices.inHouse_DB_cosy.choice) == 'yes':
38 cosyDB $inHouse_DB_choices.inHouse_DB_cosy.cosyDB
39 #end if
40 inHouse_DB_hmbc.choice ${inHouse_DB_choices.inHouse_DB_hmbc.choice}
41 #if str($inHouse_DB_choices.inHouse_DB_hmbc.choice) == 'yes':
42 hmbcDB $inHouse_DB_choices.inHouse_DB_hmbc.hmbcDB
43 #end if
44 inHouse_DB_hsqc.choice ${inHouse_DB_choices.inHouse_DB_hsqc.choice}
45 #if str($inHouse_DB_choices.inHouse_DB_hsqc.choice) == 'yes':
46 hsqcDB $inHouse_DB_choices.inHouse_DB_hsqc.hsqcDB
47 #end if
48 inHouse_DB_jres.choice ${inHouse_DB_choices.inHouse_DB_jres.choice}
49 #if str($inHouse_DB_choices.inHouse_DB_jres.choice) == 'yes':
50 jresDB $inHouse_DB_choices.inHouse_DB_jres.jresDB
51 #end if
52 inHouse_DB_tocsy.choice ${inHouse_DB_choices.inHouse_DB_tocsy.choice}
53 #if str($inHouse_DB_choices.inHouse_DB_tocsy.choice) == 'yes':
54 tocsyDB $inHouse_DB_choices.inHouse_DB_tocsy.tocsyDB
55 #end if
56 #end if
57
58 ## Tolerances
59 tolppm1 $tolppm1
60 tolppm2 $tolppm2
61 tolppmJRES $tolppmJRES
62
63
64 ## Treshold (probability score)
65 threshold $threshold
66
67 ## Unicity
68 unicity $unicity
69
70 ## Outputs
71 logOut '$logOut'
72 annotationCOSY '$annotationCOSY'
73 ppmCommunCOSY '$ppmCommunCOSY'
74 annotationJRES '$annotationJRES'
75 ppmCommunJRES '$ppmCommunJRES'
76 annotationHMBC '$annotationHMBC'
77 ppmCommunHMBC '$ppmCommunHMBC'
78 annotationHSQC '$annotationHSQC'
79 ppmCommunHSQC '$ppmCommunHSQC'
80 annotationTOCSY '$annotationTOCSY'
81 ppmCommunTOCSY '$ppmCommunTOCSY'
82 annotationCombination '$annotationCombination'
83 AnnotationGraph '$AnnotationGraph'
84
85 </command>
86
87 <inputs>
88 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
89
90 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence">
91 <option value="yes" > yes </option>
92 <option value="no" selected="true"> no </option>
93 </param>
94 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
95 <option value="yes" > yes </option>
96 <option value="no" selected="true"> no </option>
97 </param>
98 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence">
99 <option value="yes" > yes </option>
100 <option value="no" selected="true"> no </option>
101 </param>
102 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence">
103 <option value="yes" > yes </option>
104 <option value="no" selected="true"> no </option>
105 </param>
106 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence">
107 <option value="yes" > yes </option>
108 <option value="no" selected="true"> no </option>
109 </param>
110
111 <conditional name="inHouse_DB_choices">
112 <param name="choice" type="select" label="In-house database" help="Choose if you want to use use in-house database to annotate" >
113 <option value="yes" > yes </option>
114 <option value="no" selected="true"> no </option>
115 </param>
116 <when value="yes">
117 <conditional name="inHouse_DB_cosy">
118 <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" >
119 <option value="yes" > yes </option>
120 <option value="no" selected="true"> no </option>
121 </param>
122 <when value="yes">
123 <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" />
124 </when>
125 <when value="no" />
126 </conditional>
127 <conditional name="inHouse_DB_hmbc">
128 <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" >
129 <option value="yes" > yes </option>
130 <option value="no" selected="true"> no </option>
131 </param>
132 <when value="yes">
133 <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" />
134 </when>
135 <when value="no" />
136 </conditional>
137 <conditional name="inHouse_DB_hsqc">
138 <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" >
139 <option value="yes" > yes </option>
140 <option value="no" selected="true"> no </option>
141 </param>
142 <when value="yes">
143 <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" />
144 </when>
145 <when value="no" />
146 </conditional>
147 <conditional name="inHouse_DB_jres">
148 <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" >
149 <option value="yes" > yes </option>
150 <option value="no" selected="true"> no </option>
151 </param>
152 <when value="yes">
153 <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" />
154 </when>
155 <when value="no" />
156 </conditional>
157 <conditional name="inHouse_DB_tocsy">
158 <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" >
159 <option value="yes" > yes </option>
160 <option value="no" selected="true"> no </option>
161 </param>
162 <when value="yes">
163 <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" />
164 </when>
165 <when value="no" />
166 </conditional>
167 </when>
168 <when value="no" />
169 </conditional>
170
171 <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" />
172 <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" />
173 <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)" />
174
175 <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" />
176
177 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="">
178 <option value="no">No</option>
179 <option value="yes"></option>
180 </param>
181
182 </inputs>
183
184 <outputs>
185 <data format="txt" name="logOut" label="${tool.name}_log" />
186 <data format="tabular" name="annotationCOSY" label="annotationCosy" >
187 <filter> cosy_2dsequences != "no" </filter>
188 </data>
189 <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" >
190 <filter> cosy_2dsequences != "no" </filter>
191 </data>
192
193 <data format="tabular" name="annotationJRES" label="annotationJres" >
194 <filter> jres_2dsequences != "no" </filter>
195 </data>
196 <data format="tabular" name="ppmCommunJRES" label="duplicateJres" >
197 <filter> jres_2dsequences != "no" </filter>
198 </data>
199
200 <data format="tabular" name="annotationHMBC" label="annotationHmbc" >
201 <filter> hmbc_2dsequences != "no" </filter>
202 </data>
203 <data format="tabular" name="ppmCommunHMBC" label="duplicateHmbc" >
204 <filter> hmbc_2dsequences != "no" </filter>
205 </data>
206
207 <data format="tabular" name="annotationHSQC" label="annotationHsqc" >
208 <filter> hsqc_2dsequences != "no" </filter>
209 </data>
210 <data format="tabular" name="ppmCommunHSQC" label="duplicateHsqc" >
211 <filter> hsqc_2dsequences != "no" </filter>
212 </data>
213
214 <data format="tabular" name="annotationTOCSY" label="annotationTocsy" >
215 <filter> tocsy_2dsequences != "no" </filter>
216 </data>
217 <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" >
218 <filter> tocsy_2dsequences != "no" </filter>
219 </data>
220
221 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
222 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
223 </outputs>
224 <tests>
225 <test>
226 <param name="zip_xlsfile" value="Template_melange.xlsm" ftype="xlsx"/>
227 <param name="cosy_2dsequences" value="no"/>
228 <param name="jres_2dsequences" value="yes"/>
229 <param name="hmbc_2dsequences" value="no"/>
230 <param name="hsqc_2dsequences" value="yes"/>
231 <param name="tocsy_2dsequences" value="no"/>
232 <param name="tocsy_2dsequences" value="no"/>
233 <param name="inHouse_DB_choices.choice" value="no"/>
234 <param name="tolppm1" value="0.01"/>
235 <param name="tolppm2" value="0.5"/>
236 <param name="tolppmJRES" value="0.002"/>
237 <param name="threshold" value="0.3"/>
238 <param name="unicity" value="no"/>
239 <output name="annotationJRES" file="annotationJres.tabular"/>
240 <output name="ppmCommunJRES" file="duplicateJres.tabular"/>
241 <output name="annotationHSQC" file="annotationHsqc.tabular"/>
242 <output name="ppmCommunHSQC" file="duplicateHsqc.tabular"/>
243 <output name="annotationCombination" file="2DNMR_Annotation_annotationCombination.tabular"/>
244 </test>
245 </tests>
246 <help>
247
248 .. class:: infomark
249
250 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
251
252 .. class:: infomark
253
254
255 ---------------------------------------------------
256
257 ============================
258 Bidimensional NMR Annotation
259 ============================
260
261 -----------
262 Description
263 -----------
264
265 BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
266
267 -----------------
268 Workflow position
269 -----------------
270
271 **Upstream tools**
272
273 ========================= ================= ======= =========
274 Name output file format parameter
275 ========================= ================= ======= =========
276 NA NA NA NA
277 ========================= ================= ======= =========
278
279
280 **Downstream tools**
281
282 ========================= ================= ======= =========
283 Name output file format parameter
284 ========================= ================= ======= =========
285 NA NA NA NA
286 ========================= ================= ======= =========
287
288
289
290 -----------
291 Input files
292 -----------
293
294 +---------------------------+------------+
295 | Parameter : num + label | Format |
296 +===========================+============+
297 | 1 : Choose your inputs | xlsx |
298 +---------------------------+------------+
299
300 **Choose your inputs**
301 | xlsx file can include several peak lists, coming from several 2D NMR sequences
302 |
303
304 .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png
305
306 ----------
307 Parameters
308 ----------
309
310 Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s)
311 | COSY: yes/no
312 | JRES: yes/no
313 | HMBC: yes/no
314 | HSQC: yes/no
315 | TOCSY: yes/no
316 | Default value is no
317 |
318
319 In-house databases
320 | Use of your own databases to annotate peak list(s)
321 | 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
322 | Select one or more in-house database
323 |
324
325
326 Tolerances
327 | tolppm1: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the x-axis
328 | tolppm2: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the y-axis
329 | tolppmJRES: Maximum variation of the chemical shift (due to experimental conditions) of a peak for the JRES sequence
330 | Default values: 0.01 and 0.01 ppm; 0.002 Hz
331 |
332
333
334 Threshold
335 | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
336 | Default value: 0
337 |
338
339
340 Unicity of annotation
341 | All the peaks assigned to more than one metabolite are removed
342 |
343
344
345 ------------
346 Output files
347 ------------
348 COSY
349 | tabular outputs
350 | 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
351 | 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
352 | Only display if COSY was chosen
353 |
354
355
356 JRES
357 | tabular outputs
358 | 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
359 | 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
360 | Only display if JRES was chosen
361 |
362
363
364 HMBC
365 | tabular outputs
366 | 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
367 | 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
368 | Only display if HMBC was chosen
369 |
370
371
372 HSQC
373 | tabular outputs
374 | 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
375 | 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
376 | Only display if HSQC was chosen
377 |
378
379
380 TOCSY
381 | tabular outputs
382 | 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
383 | 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
384 | Only display if TOCSY was chosen
385 |
386
387
388 annotationCombination
389 | tabular outputs
390 | 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
391 | Depends on the chosen sequences
392 | Only display if 2 or more sequences have be chosen
393
394
395 AnnotationGraph.pdf
396 | pdf output
397 | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
398
399
400
401 ---------------------------------------------------
402
403 -------
404 Example
405 -------
406 Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
407
408 .. image:: ./static/images/OutputsExampleMix.png
409 :width: 500
410
411 </help>
412 <citations>
413 <citation type="doi">10.1093/bioinformatics/btu813</citation>
414 </citations>
415
416 </tool>