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author lain
date Tue, 06 Dec 2022 10:18:10 +0000
parents 2937e72e5891
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19:2937e72e5891 20:ce94e7a141bb
1 <tool id="xseeker_preparator" name="XSeeker Preparator" version="1.3.0"> 1 <tool id="xseeker_preparator" name="XSeeker Preparator" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>prepares RData file from XCMS+CAMERA for XSeeker</description> 2 <description>prepares RData file from XCMS+CAMERA for XSeeker</description>
3 <macros>
4 <token name="@VERSION@">1.3.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <edam_operations> 7 <edam_operations>
4 <edam_operation>operation_1812</edam_operation> 8 <edam_operation>operation_1812</edam_operation>
5 <edam_operation>operation_0335</edam_operation> 9 <edam_operation>operation_0335</edam_operation>
6 </edam_operations> 10 </edam_operations>
7 <requirements> 11 <requirements>
8 <requirement type="package" >bioconductor-xcms</requirement> 12 <requirement type="package" version="4.1.3">r-base</requirement>
9 <requirement type="package" version="1.48.0">bioconductor-camera</requirement> 13 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
10 <requirement type="package" >git</requirement>
11 <requirement type="package" >r-blob</requirement>
12 <requirement type="package" >r-dbi</requirement>
13 <requirement type="package" >r-fst</requirement>
14 <requirement type="package" >r-optparse</requirement>
15 <requirement type="package" >r-stringr</requirement>
16 <requirement type="package" >r-purrr</requirement>
17 <requirement type="package" >r-rsqlite</requirement>
18 <requirement type="package" >r-dbmodelr</requirement>
19 <!--
20 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
21 <requirement type="package" version="1.48.0">bioconductor-camera</requirement> 14 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
22 <requirement type="package" version="2.29.2">git</requirement> 15 <requirement type="package" version="2.29.2">git</requirement>
23 <requirement type="package" version="1.2.1">r-blob</requirement> 16 <requirement type="package" version="1.2.3">r-blob</requirement>
24 <requirement type="package" version="1.1.0">r-dbi</requirement> 17 <requirement type="package" version="1.1.3">r-dbi</requirement>
25 <requirement type="package" version="0.9.4">r-fst</requirement> 18 <requirement type="package" version="0.9.8">r-fst</requirement>
26 <requirement type="package" version="1.6.6">r-optparse</requirement> 19 <requirement type="package" version="1.6.6">r-optparse</requirement>
27 <requirement type="package" version="1.4.0">r-stringr</requirement> 20 <requirement type="package" version="1.4.0">r-stringr</requirement>
28 <requirement type="package" version="0.3.4">r-purrr</requirement> 21 <requirement type="package" version="0.3.5">r-purrr</requirement>
29 <requirement type="package" version="2.2.1">r-rsqlite</requirement> 22 <requirement type="package" version="2.2.18">r-rsqlite</requirement>
30 <requirement type="package" version="0.2.0">r-dbmodelr</requirement> 23 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
31 -->
32 </requirements> 24 </requirements>
33 <stdio> 25 <stdio>
34 <exit_code 26 <exit_code
35 range="1" 27 range="1"
36 level="warning" 28 level="warning"
65 #if $database.models.kind == "default" 57 #if $database.models.kind == "default"
66 --models '${base_config}' 58 --models '${base_config}'
67 #else 59 #else
68 --models '${database.models.url}' 60 --models '${database.models.url}'
69 #end if 61 #end if
70 #if $class_column 62 #if $class
71 --class '${class_column}' 63 --class '${class}'
72 #end if 64 #end if
73 ]]> 65 ]]>
74 </command> 66 </command>
67 <configfiles>
68 <configfile name="base_config">
69 <![CDATA[
70 tryCatch({
71 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
72 }, error=function(e) {
73 stop("Please, install DBModelR before you source this file.")
74 })
75 list(
76 adduct = DBModelR::ModelDefinition(
77 table = "adduct",
78 fields = list(
79 name = "TEXT",
80 mass = "FLOAT",
81 charge = "INTEGER",
82 multi = "INTEGER",
83 formula_add = "TEXT",
84 formula_ded = "TEXT",
85 sign = "TEXT",
86 oidscore = "INTEGER",
87 quasi = "INTEGER",
88 ips = "FLOAT"
89 )
90 ),
91 cluster = DBModelR::ModelDefinition(
92 table = "cluster",
93 fields = list(
94 clusterID = "INTEGER",
95 formula = "TEXT",
96 annotation = "TEXT",
97 coeff = "FLOAT",
98 r_squared = "FLOAT",
99 charge = "INTEGER",
100 mean_rt = "FLOAT",
101 score = "FLOAT",
102 deviation = "FLOAT",
103 status = "TEXT",
104 # adduct = "TEXT",
105 curent_group = "INTEGER",
106 pc_group = "INTEGER",
107 align_group = "INTEGER",
108 xcms_group = "INTEGER"
109 ),
110 one = list("compound", "adduct"),
111 many = list("sample")
112 ),
113 compound = DBModelR::ModelDefinition(
114 table = "compound",
115 fields = list(
116 name = "TEXT",
117 common_name = "TEXT",
118 formula = "TEXT",
119 charge = "INTEGER",
120 date = "TEXT",
121 mz = "FLOAT"
122 )
123 ),
124 feature = DBModelR::ModelDefinition(
125 table = "feature",
126 fields = list(
127 featureID = "INTEGER",
128 mz = "FLOAT",
129 mz_min = "FLOAT",
130 mz_max = "FLOAT",
131 rt = "FLOAT",
132 rt_min = "FLOAT",
133 rt_max = "FLOAT",
134 int_o = "FLOAT",
135 int_b = "FLOAT",
136 max_o = "FLOAT",
137 iso = "TEXT",
138 abundance = "FLOAT"
139 ),
140 one = list("cluster"),
141 many = list("sample")
142 ),
143 instrument = DBModelR::ModelDefinition(
144 table = "instrument",
145 fields = list(
146 model = "TEXT",
147 manufacturer = "TEXT",
148 analyzer = "TEXT",
149 detector_type = "TEXT",
150 ion_source = "TEXT"
151 )
152 ),
153 instrument_config = DBModelR::ModelDefinition(
154 table = "instrument_config",
155 fields = list(
156 resolution = "TEXT",
157 agc_target = "TEXT",
158 maximum_IT = "TEXT",
159 number_of_scan_range = "TEXT",
160 scan_range = "TEXT",
161 version = "TEXT"
162 )
163 ),
164 project = DBModelR::ModelDefinition(
165 table = "project",
166 fields = list(
167 name = "TEXT",
168 comment = "TEXT"
169 ),
170 one = list("sample")
171 ),
172 sample = DBModelR::ModelDefinition(
173 table = "sample",
174 fields = list(
175 name = "TEXT",
176 path = "TEXT",
177 polarity = "TEXT",
178 kind = "TEXT", ## rdata or mxml or enriched_rdata
179 raw = "BLOB"
180 ),
181 one = list(
182 "peak_picking_parameters",
183 "pairing_parameters",
184 "alignmenmt_parameters",
185 "camera_parameters",
186 "instrument",
187 "instrument_config",
188 "software",
189 "smol_xcms_set"
190 )
191 ),
192 smol_xcms_set = DBModelR::ModelDefinition(
193 table = "smol_xcms_set",
194 fields = list(
195 raw = "BLOB"
196 )
197 ),
198 software = DBModelR::ModelDefinition(
199 table = "software",
200 fields = list(
201 name = "TEXT",
202 version = "TEXT"
203 )
204 ),
205 peak_picking_parameters = DBModelR::ModelDefinition(
206 table = "peak_picking_parameters",
207 fields = list(
208 ppm = "FLOAT",
209 peakwidth = "TEXT",
210 snthresh = "TEXT",
211 prefilterStep = "TEXT",
212 prefilterLevel = "TEXT",
213 mzdiff = "TEXT",
214 fitgauss = "TEXT",
215 noise = "TEXT",
216 mzCenterFun = "TEXT",
217 integrate = "INTEGER",
218 firstBaselineCheck = "TEXT",
219 snthreshIsoROIs = "TEXT",
220 maxCharge = "INTEGER",
221 maxIso = "INTEGER",
222 mzIntervalExtension = "TEXT"
223 )
224 ),
225 alignmenmt_parameters = DBModelR::ModelDefinition(
226 table = "alignmenmt_parameters",
227 fields = list(
228 binSize = "TEXT",
229 centerSample = "TEXT",
230 response = "TEXT",
231 distFun = "TEXT",
232 gapInit = "TEXT",
233 gapExtend = "TEXT",
234 factorDiag = "TEXT",
235 factorGap = "TEXT",
236 localAlignment = "INTEGER",
237 initPenalty = "TEXT",
238 bw = "TEXT",
239 minFraction = "TEXT",
240 minSamples = "TEXT",
241 maxFeatures = "TEXT"
242 )
243 )
244 )
245 ]]>
246 </configfile>
247 </configfiles>
75 <inputs> 248 <inputs>
76 <param 249 <param
77 name="input" 250 argument="input"
78 type="data" 251 type="data"
79 multiple="false" 252 multiple="false"
80 label="Rdata to prepare"
81 optional="false" 253 optional="false"
82 format="rdata" 254 format="rdata"
255 label="Rdata to prepare"
256 help="
257 This rdata must be produced by a xcms+camera processing
258 and original files must still be in the history.
259 "
83 > 260 >
84 </param> 261 </param>
85 <param 262 <param
86 name="class_column" 263 argument="class"
87 type="text" 264 type="text"
88 value="" 265 value=""
89 label="Column class name" 266 label="Column class name"
90 help=" 267 help="
91 The name of the column containing the classes - 268 The name of the column containing the classes -
92 leave empty to let xsprep guess 269 leave empty to let XSeeker Preparator guess
93 " 270 "
94 optional="true" 271 optional="true"
95 > 272 >
96 </param> 273 </param>
97 <section name="samples" title="Samples Options" expanded="false"> 274 <section name="samples" title="Samples Options" expanded="false">
115 <option value="G" selected="true">General</option> 292 <option value="G" selected="true">General</option>
116 <option value="H">Halogenates</option> 293 <option value="H">Halogenates</option>
117 </param> 294 </param>
118 <conditional name="base"> 295 <conditional name="base">
119 <param name="kind" type="select" label="File containing compound's type"> 296 <param name="kind" type="select" label="File containing compound's type">
120 <option value="none" selected="true">None (deafult)</option> 297 <option value="none" selected="true">None (default)</option>
121 <option value="tabular">tabular</option> 298 <option value="tabular">tabular</option>
122 <option value="sql">sql</option> 299 <option value="sql">sql</option>
123 </param> 300 </param>
301 <when value="none" />
302 <when value="sql" />
124 <when value="tabular"> 303 <when value="tabular">
125 <param 304 <param
126 name="tabular" 305 name="tabular"
127 type="data" 306 type="data"
128 multiple="true" 307 multiple="true"
148 <param name="kind" type="select" label="How is the database's model defined"> 327 <param name="kind" type="select" label="How is the database's model defined">
149 <option value="default" selected="true">Default (regular XSeeker Database)</option> 328 <option value="default" selected="true">Default (regular XSeeker Database)</option>
150 <option value="url">Download model file</option> 329 <option value="url">Download model file</option>
151 <option value="git">Get versionned model file</option> 330 <option value="git">Get versionned model file</option>
152 </param> 331 </param>
332 <when value="default" />
153 <when value="url"> 333 <when value="url">
154 <param name="url" type="text" format="url" label="File URL"/> 334 <param name="url" type="text" format="url" label="File URL"/>
155 </when> 335 </when>
156 <when value="git"> 336 <when value="git">
157 <param name="url" type="text" format="url" label="Repo URL"/> 337 <param name="url" type="text" format="url" label="Repo URL"/>
161 </inputs> 341 </inputs>
162 <outputs> 342 <outputs>
163 <data format="sqlite" name="output" /> 343 <data format="sqlite" name="output" />
164 <!-- <data format="xseeker.sqlite" name="output" /> --> 344 <!-- <data format="xseeker.sqlite" name="output" /> -->
165 </outputs> 345 </outputs>
166 <configfiles> 346 <help>
167 <configfile name="base_config"> 347
168 tryCatch({ 348 .. class:: infomark
169 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER")) 349
170 }, error=function(e) { 350 **Authors** Lain Pavot (lain.pavot@inrae.fr)
171 stop("Please, install DBModelR before you source this file.") 351
172 }) 352 --------------------------------------
173 list( 353
174 adduct = DBModelR::ModelDefinition( 354 ==================
175 table = "adduct", 355 XSeeker Preparator
176 fields = list( 356 ==================
177 name = "TEXT", 357
178 mass = "FLOAT", 358 -----------
179 charge = "INTEGER", 359 Description
180 multi = "INTEGER", 360 -----------
181 formula_add = "TEXT", 361
182 formula_ded = "TEXT", 362 A preparation tool to precalculate and reorginize data from XCMS+CAMERA for
183 sign = "TEXT", 363 XSeeker displayer tool to display them faster (from 30 min/some hours to some seconds).
184 oidscore = "INTEGER", 364
185 quasi = "INTEGER", 365
186 ips = "FLOAT" 366 -----------------
187 ) 367 Workflow position
188 ), 368 -----------------
189 cluster = DBModelR::ModelDefinition( 369
190 table = "cluster", 370 **Upstream tools**
191 fields = list( 371
192 clusterID = "INTEGER", 372 ================ ======================== =========== ===============
193 formula = "TEXT", 373 Name output file format parameter
194 annotation = "TEXT", 374 ================ ======================== =========== ===============
195 coeff = "FLOAT", 375 CAMERA rdata.camera.quick rdata
196 r_squared = "FLOAT", 376 ================ ======================== =========== ===============
197 charge = "INTEGER", 377
198 mean_rt = "FLOAT", 378
199 score = "FLOAT", 379 **Downstream tools**
200 deviation = "FLOAT", 380
201 status = "TEXT", 381 ================ ======================== =========== ===============
202 # adduct = "TEXT", 382 Name output file format parameter
203 curent_group = "INTEGER", 383 ================ ======================== =========== ===============
204 pc_group = "INTEGER", 384 XSeeker sqlite sqlite3 NA
205 align_group = "INTEGER", 385 ================ ======================== =========== ===============
206 xcms_group = "INTEGER" 386
207 ), 387
208 one = list("compound", "adduct"), 388
209 many = list("sample") 389 -----------
210 ), 390 Input files
211 compound = DBModelR::ModelDefinition( 391 -----------
212 table = "compound", 392
213 fields = list( 393 Takes a rdata outputed by camera (after xcms) as input. The rdata has must have
214 name = "TEXT", 394 been produced using some mzml files - mxml files which must still be present
215 common_name = "TEXT", 395 in the history when doing xseekerpreparator:
216 formula = "TEXT", 396 The rdata contains only some data and the paths to the original mzml files.
217 charge = "INTEGER", 397 These mzml files contains a lot of usefull informations needed to prepare
218 date = "TEXT", 398 the data for XSeeker. These files are not given as input, but are still
219 mz = "FLOAT" 399 needed.
220 ) 400
221 ), 401 ----------
222 feature = DBModelR::ModelDefinition( 402 Parameters
223 table = "feature", 403 ----------
224 fields = list( 404 Column class name:
225 featureID = "INTEGER", 405 - the name of the column that defines classes in your sample metadata.
226 mz = "FLOAT", 406 Sample options:
227 mz_min = "FLOAT", 407 - provide mzml file names to process. Other files defined in the rdata will
228 mz_max = "FLOAT", 408 not be processed, and will not be available in xseeker.
229 rt = "FLOAT", 409 Database Options:
230 rt_min = "FLOAT", 410 - provide the molecular family you want to annotate, a compound file.
231 rt_max = "FLOAT", 411 - The database's model can be re-defined - only for devs users.
232 int_o = "FLOAT", 412
233 int_b = "FLOAT", 413 ------------
234 max_o = "FLOAT", 414 Output files
235 iso = "TEXT", 415 ------------
236 abundance = "FLOAT" 416 An SQLite3 file is a database file that organizes data in such a way it is
237 ), 417 easily stored, filtered, modified, retrieved.
238 one = list("cluster"), 418 </help>
239 many = list("sample") 419 <citations></citations>
240 ),
241 instrument = DBModelR::ModelDefinition(
242 table = "instrument",
243 fields = list(
244 model = "TEXT",
245 manufacturer = "TEXT",
246 analyzer = "TEXT",
247 detector_type = "TEXT",
248 ion_source = "TEXT"
249 )
250 ),
251 instrument_config = DBModelR::ModelDefinition(
252 table = "instrument_config",
253 fields = list(
254 resolution = "TEXT",
255 agc_target = "TEXT",
256 maximum_IT = "TEXT",
257 number_of_scan_range = "TEXT",
258 scan_range = "TEXT",
259 version = "TEXT"
260 )
261 ),
262 project = DBModelR::ModelDefinition(
263 table = "project",
264 fields = list(
265 name = "TEXT",
266 comment = "TEXT"
267 ),
268 one = list("sample")
269 ),
270 sample = DBModelR::ModelDefinition(
271 table = "sample",
272 fields = list(
273 name = "TEXT",
274 path = "TEXT",
275 polarity = "TEXT",
276 kind = "TEXT", ## rdata or mxml or enriched_rdata
277 raw = "BLOB"
278 ),
279 one = list(
280 "peak_picking_parameters",
281 "pairing_parameters",
282 "alignmenmt_parameters",
283 "camera_parameters",
284 "instrument",
285 "instrument_config",
286 "software",
287 "smol_xcms_set"
288 )
289 ),
290 smol_xcms_set = DBModelR::ModelDefinition(
291 table = "smol_xcms_set",
292 fields = list(
293 raw = "BLOB"
294 )
295 ),
296 software = DBModelR::ModelDefinition(
297 table = "software",
298 fields = list(
299 name = "TEXT",
300 version = "TEXT"
301 )
302 ),
303 peak_picking_parameters = DBModelR::ModelDefinition(
304 table = "peak_picking_parameters",
305 fields = list(
306 ppm = "FLOAT",
307 peakwidth = "TEXT",
308 snthresh = "TEXT",
309 prefilterStep = "TEXT",
310 prefilterLevel = "TEXT",
311 mzdiff = "TEXT",
312 fitgauss = "TEXT",
313 noise = "TEXT",
314 mzCenterFun = "TEXT",
315 integrate = "INTEGER",
316 firstBaselineCheck = "TEXT",
317 snthreshIsoROIs = "TEXT",
318 maxCharge = "INTEGER",
319 maxIso = "INTEGER",
320 mzIntervalExtension = "TEXT"
321 )
322 ),
323 alignmenmt_parameters = DBModelR::ModelDefinition(
324 table = "alignmenmt_parameters",
325 fields = list(
326 binSize = "TEXT",
327 centerSample = "TEXT",
328 response = "TEXT",
329 distFun = "TEXT",
330 gapInit = "TEXT",
331 gapExtend = "TEXT",
332 factorDiag = "TEXT",
333 factorGap = "TEXT",
334 localAlignment = "INTEGER",
335 initPenalty = "TEXT",
336 bw = "TEXT",
337 minFraction = "TEXT",
338 minSamples = "TEXT",
339 maxFeatures = "TEXT"
340 )
341 )
342 )
343 </configfile>
344 </configfiles>
345 </tool> 420 </tool>