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comparison nmr_annotation2d/annotationRmn2D_xml.xml @ 1:a4d2b1926e13 draft

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author marie-tremblay-metatoul
date Tue, 04 Feb 2020 04:05:38 -0500
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1 <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0"> 1 <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0">
2 2
3 <description> Annotation of complex mixture bidimensional NMR spectra </description> 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>
4 13
5 <stdio> 14 <stdio>
6 <exit_code range="1:" level="fatal" /> 15 <exit_code range="1:" level="fatal" />
7 </stdio> 16 </stdio>
8 17
9 <command> 18 <command>
10 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds 19 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
11 Rscript '$__tool_directory__/annotationRmn2DWrapper.R' 20 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
12 21
13 22
14 ## XLS file 23 ## XLS file
15 xlsfile $zip_xlsfile 24 xlsfile '$zip_xlsfile'
16 25
17 ## 2D-NMR sequences to annotate 26 ## 2D-NMR sequences to annotate
18 cosy_2dsequences $cosy_2dsequences 27 cosy_2dsequences $cosy_2dsequences
19 jres_2dsequences $jres_2dsequences 28 jres_2dsequences $jres_2dsequences
20 hmbc_2dsequences $hmbc_2dsequences 29 hmbc_2dsequences $hmbc_2dsequences
21 hsqc_2dsequences $hsqc_2dsequences 30 hsqc_2dsequences $hsqc_2dsequences
22 tocsy_2dsequences $tocsy_2dsequences 31 tocsy_2dsequences $tocsy_2dsequences
23 32
24 ## In-house databases 33 ## In-house databases
25 inHouse_DB_choices.choice ${inHouse_DB_choices.choice} 34 inHouse_DB_choices.choice ${inHouse_DB_choices.choice}
26 #if str($inHouse_DB_choices.choice) == 'yes': 35 #if str($inHouse_DB_choices.choice) == 'yes':
27 inHouse_DB_cosy.choice ${inHouse_DB_cosy.choice} 36 inHouse_DB_cosy.choice ${inHouse_DB_choices.inHouse_DB_cosy.choice}
28 #if str($inHouse_DB_cosy.choice) == 'yes': 37 #if str($inHouse_DB_choices.inHouse_DB_cosy.choice) == 'yes':
29 cosyDB $cosyDB 38 cosyDB $inHouse_DB_choices.inHouse_DB_cosy.cosyDB
30 #end if 39 #end if
31 inHouse_DB_hmbc.choice ${inHouse_DB_hmbc.choice} 40 inHouse_DB_hmbc.choice ${inHouse_DB_choices.inHouse_DB_hmbc.choice}
32 #if str($inHouse_DB_hmbc.choice) == 'yes': 41 #if str($inHouse_DB_choices.inHouse_DB_hmbc.choice) == 'yes':
33 hmbcDB $hmbcDB 42 hmbcDB $inHouse_DB_choices.inHouse_DB_hmbc.hmbcDB
34 #end if 43 #end if
35 inHouse_DB_hsqc.choice ${inHouse_DB_hsqc.choice} 44 inHouse_DB_hsqc.choice ${inHouse_DB_choices.inHouse_DB_hsqc.choice}
36 #if str($inHouse_DB_hsqc.choice) == 'yes': 45 #if str($inHouse_DB_choices.inHouse_DB_hsqc.choice) == 'yes':
37 hsqcDB $hsqcDB 46 hsqcDB $inHouse_DB_choices.inHouse_DB_hsqc.hsqcDB
38 #end if 47 #end if
39 inHouse_DB_jres.choice ${inHouse_DB_jres.choice} 48 inHouse_DB_jres.choice ${inHouse_DB_choices.inHouse_DB_jres.choice}
40 #if str($inHouse_DB_jres.choice) == 'yes': 49 #if str($inHouse_DB_choices.inHouse_DB_jres.choice) == 'yes':
41 jresDB $jresDB 50 jresDB $inHouse_DB_choices.inHouse_DB_jres.jresDB
42 #end if 51 #end if
43 inHouse_DB_tocsy.choice ${inHouse_DB_tocsy.choice} 52 inHouse_DB_tocsy.choice ${inHouse_DB_choices.inHouse_DB_tocsy.choice}
44 #if str($inHouse_DB_tocsy.choice) == 'yes': 53 #if str($inHouse_DB_choices.inHouse_DB_tocsy.choice) == 'yes':
45 tocsyDB $tocsyDB 54 tocsyDB $inHouse_DB_choices.inHouse_DB_tocsy.tocsyDB
46 #end if 55 #end if
47 #end if 56 #end if
48 57
49 ## Tolerances 58 ## Tolerances
50 tolppm1 $tolppm1 59 tolppm1 $tolppm1
51 tolppm2 $tolppm2 60 tolppm2 $tolppm2
52 tolppmJRES $tolppmJRES 61 tolppmJRES $tolppmJRES
53 62
54 63
55 ## Treshold (probability score) 64 ## Treshold (probability score)
56 threshold $threshold 65 threshold $threshold
57 66
58 ## Unicity 67 ## Unicity
59 unicity $unicity 68 unicity $unicity
60 69
61 ## Outputs 70 ## Outputs
62 logOut $logOut 71 logOut '$logOut'
63 annotationCOSY $annotationCOSY 72 annotationCOSY '$annotationCOSY'
64 ppmCommunCOSY $ppmCommunCOSY 73 ppmCommunCOSY '$ppmCommunCOSY'
65 annotationJRES $annotationJRES 74 annotationJRES '$annotationJRES'
66 ppmCommunJRES $ppmCommunJRES 75 ppmCommunJRES '$ppmCommunJRES'
67 annotationHMBC $annotationHMBC 76 annotationHMBC '$annotationHMBC'
68 ppmCommunHMBC $ppmCommunHMBC 77 ppmCommunHMBC '$ppmCommunHMBC'
69 annotationHSQC $annotationHSQC 78 annotationHSQC '$annotationHSQC'
70 ppmCommunHSQC $ppmCommunHSQC 79 ppmCommunHSQC '$ppmCommunHSQC'
71 annotationTOCSY $annotationTOCSY 80 annotationTOCSY '$annotationTOCSY'
72 ppmCommunTOCSY $ppmCommunTOCSY 81 ppmCommunTOCSY '$ppmCommunTOCSY'
73 annotationCombination $annotationCombination 82 annotationCombination '$annotationCombination'
74 AnnotationGraph $AnnotationGraph 83 AnnotationGraph '$AnnotationGraph'
75 84
76 </command> 85 </command>
77 86
78 <inputs> 87 <inputs>
79 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" /> 88 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
80 89
81 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence"> 90 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence">
82 <option value="yes" > yes </option> 91 <option value="yes" > yes </option>
83 <option value="no" selected="true"> no </option> 92 <option value="no" selected="true"> no </option>
84 </param> 93 </param>
85 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence"> 94 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
86 <option value="yes" > yes </option> 95 <option value="yes" > yes </option>
87 <option value="no" selected="true"> no </option> 96 <option value="no" selected="true"> no </option>
88 </param> 97 </param>
89 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence"> 98 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence">
90 <option value="yes" > yes </option> 99 <option value="yes" > yes </option>
91 <option value="no" selected="true"> no </option> 100 <option value="no" selected="true"> no </option>
92 </param> 101 </param>
93 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence"> 102 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence">
94 <option value="yes" > yes </option> 103 <option value="yes" > yes </option>
95 <option value="no" selected="true"> no </option> 104 <option value="no" selected="true"> no </option>
96 </param> 105 </param>
97 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence"> 106 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence">
98 <option value="yes" > yes </option> 107 <option value="yes" > yes </option>
99 <option value="no" selected="true"> no </option> 108 <option value="no" selected="true"> no </option>
100 </param> 109 </param>
101 110
102 <conditional name="inHouse_DB_choices"> 111 <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" > 112 <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> 113 <option value="yes" > yes </option>
105 <option value="no" selected="true"> no </option> 114 <option value="no" selected="true"> no </option>
106 </param> 115 </param>
107 <when value="yes"> 116 <when value="yes">
108 <conditional name="inHouse_DB_cosy"> 117 <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" > 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" >
110 <option value="yes" > yes </option> 119 <option value="yes" > yes </option>
111 <option value="no" selected="true"> no </option> 120 <option value="no" selected="true"> no </option>
112 </param> 121 </param>
113 <when value="yes"> 122 <when value="yes">
114 <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" /> 123 <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" />
115 </when> 124 </when>
116 </conditional> 125 <when value="no" />
117 <conditional name="inHouse_DB_hmbc"> 126 </conditional>
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" > 127 <conditional name="inHouse_DB_hmbc">
119 <option value="yes" > yes </option> 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" >
120 <option value="no" selected="true"> no </option> 129 <option value="yes" > yes </option>
121 </param> 130 <option value="no" selected="true"> no </option>
122 <when value="yes"> 131 </param>
123 <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" /> 132 <when value="yes">
124 </when> 133 <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" />
125 </conditional> <conditional name="inHouse_DB_hsqc"> 134 </when>
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" > 135 <when value="no" />
127 <option value="yes" > yes </option> 136 </conditional>
128 <option value="no" selected="true"> no </option> 137 <conditional name="inHouse_DB_hsqc">
129 </param> 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" >
130 <when value="yes"> 139 <option value="yes" > yes </option>
131 <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" /> 140 <option value="no" selected="true"> no </option>
132 </when> 141 </param>
133 </conditional> <conditional name="inHouse_DB_jres"> 142 <when value="yes">
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" > 143 <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" />
135 <option value="yes" > yes </option> 144 </when>
136 <option value="no" selected="true"> no </option> 145 <when value="no" />
137 </param> 146 </conditional>
138 <when value="yes"> 147 <conditional name="inHouse_DB_jres">
139 <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" /> 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" >
140 </when> 149 <option value="yes" > yes </option>
141 </conditional> 150 <option value="no" selected="true"> no </option>
142 <conditional name="inHouse_DB_tocsy"> 151 </param>
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" > 152 <when value="yes">
144 <option value="yes" > yes </option> 153 <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" />
145 <option value="no" selected="true"> no </option> 154 </when>
146 </param> 155 <when value="no" />
147 <when value="yes"> 156 </conditional>
148 <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" /> 157 <conditional name="inHouse_DB_tocsy">
149 </when> 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" >
150 </conditional> 159 <option value="yes" > yes </option>
151 </when> 160 <option value="no" selected="true"> no </option>
152 <when value="no" /> 161 </param>
153 </conditional> 162 <when value="yes">
154 163 <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" />
155 <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" /> 164 </when>
156 <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" /> 165 <when value="no" />
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)" /> 166 </conditional>
158 167 </when>
159 <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" /> 168 <when value="no" />
160 169 </conditional>
161 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help=""> 170
162 <option value="no">No</option> 171 <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" />
163 <option value="yes"></option> 172 <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" />
164 </param> 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)" />
165 174
166 </inputs> 175 <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" />
167 176
168 <outputs> 177 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="">
169 <data format="txt" name="logOut" label="${tool.name}_log" /> 178 <option value="no">No</option>
179 <option value="yes"></option>
180 </param>
181
182 </inputs>
183
184 <outputs>
185 <data format="txt" name="logOut" label="${tool.name}_log" />
170 <data format="tabular" name="annotationCOSY" label="annotationCosy" > 186 <data format="tabular" name="annotationCOSY" label="annotationCosy" >
171 <filter> cosy_2dsequences != "no" </filter> 187 <filter> cosy_2dsequences != "no" </filter>
172 </data> 188 </data>
173 <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" > 189 <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" >
174 <filter> cosy_2dsequences != "no" </filter> 190 <filter> cosy_2dsequences != "no" </filter>
201 <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" > 217 <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" >
202 <filter> tocsy_2dsequences != "no" </filter> 218 <filter> tocsy_2dsequences != "no" </filter>
203 </data> 219 </data>
204 220
205 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" /> 221 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
206 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" /> 222 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
207 </outputs> 223 </outputs>
208 224 <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>
209 <help> 246 <help>
210 247
211 .. class:: infomark 248 .. class:: infomark
212 249
213 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou 250 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
224 ----------- 261 -----------
225 Description 262 Description
226 ----------- 263 -----------
227 264
228 BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation 265 BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
229 266
230 ----------------- 267 -----------------
231 Workflow position 268 Workflow position
232 ----------------- 269 -----------------
233 270
234 **Upstream tools** 271 **Upstream tools**
235 272
236 ========================= ================= ======= ========= 273 ========================= ================= ======= =========
237 Name output file format parameter 274 Name output file format parameter
238 ========================= ================= ======= ========= 275 ========================= ================= ======= =========
239 NA NA NA NA 276 NA NA NA NA
240 ========================= ================= ======= ========= 277 ========================= ================= ======= =========
241 278
242 279
243 **Downstream tools** 280 **Downstream tools**
244 281
245 ========================= ================= ======= ========= 282 ========================= ================= ======= =========
246 Name output file format parameter 283 Name output file format parameter
247 ========================= ================= ======= ========= 284 ========================= ================= ======= =========
248 NA NA NA NA 285 NA NA NA NA
249 ========================= ================= ======= ========= 286 ========================= ================= ======= =========
250 287
251 288
252 289
253 ----------- 290 -----------
261 +---------------------------+------------+ 298 +---------------------------+------------+
262 299
263 **Choose your inputs** 300 **Choose your inputs**
264 | xlsx file can include several peak lists, coming from several 2D NMR sequences 301 | xlsx file can include several peak lists, coming from several 2D NMR sequences
265 | 302 |
266 303
267 .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png 304 .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png
268 305
269 ---------- 306 ----------
270 Parameters 307 Parameters
271 ---------- 308 ----------
272 309
273 Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s) 310 Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s)
274 | COSY: yes/no 311 | COSY: yes/no
275 | JRES: yes/no 312 | JRES: yes/no
276 | HMBC: yes/no 313 | HMBC: yes/no
277 | HSQC: yes/no 314 | HSQC: yes/no
281 318
282 In-house databases 319 In-house databases
283 | Use of your own databases to annotate peak list(s) 320 | 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 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
285 | Select one or more in-house database 322 | Select one or more in-house database
286 | 323 |
287 324
288 325
289 Tolerances 326 Tolerances
290 | tolppm1: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the x-axis 327 | 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 328 | 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 329 | 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 330 | Default values: 0.01 and 0.01 ppm; 0.002 Hz
294 | 331 |
295 332
296 333
297 Threshold 334 Threshold
298 | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed 335 | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
356 393
357 394
358 AnnotationGraph.pdf 395 AnnotationGraph.pdf
359 | pdf output 396 | pdf output
360 | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites 397 | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
361 398
362 399
363 400
364 --------------------------------------------------- 401 ---------------------------------------------------
365 402
366 ------- 403 -------
368 ------- 405 -------
369 Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds 406 Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
370 407
371 .. image:: ./static/images/OutputsExampleMix.png 408 .. image:: ./static/images/OutputsExampleMix.png
372 :width: 500 409 :width: 500
373 410
374 </help> 411 </help>
375 412 <citations>
413 <citation type="doi">10.1093/bioinformatics/btu813</citation>
414 </citations>
415
376 </tool> 416 </tool>