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comparison XSeekerPreparator.xml @ 19:2937e72e5891 draft

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" master branch Updating"
author lain
date Tue, 18 Oct 2022 12:57:28 +0000
parents 2c7e7fd1f740
children ce94e7a141bb
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18:2c7e7fd1f740 19:2937e72e5891
1 <tool id="xseeker_preparator" 1 <tool id="xseeker_preparator" name="XSeeker Preparator" version="1.3.0">
2 name="XSeeker Preparator" 2 <description>prepares RData file from XCMS+CAMERA for XSeeker</description>
3 version="1.2.4"
4 >
5 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
6
7 <edam_operations> 3 <edam_operations>
8 <edam_operation>operation_1812</edam_operation> 4 <edam_operation>operation_1812</edam_operation>
9 <edam_operation>operation_0335</edam_operation> 5 <edam_operation>operation_0335</edam_operation>
10 </edam_operations> 6 </edam_operations>
11
12 <requirements> 7 <requirements>
13 <requirement type="package" >bioconductor-xcms</requirement> 8 <requirement type="package" >bioconductor-xcms</requirement>
14 <requirement type="package" version="1.48.0">bioconductor-camera</requirement> 9 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
15 <requirement type="package" >git</requirement> 10 <requirement type="package" >git</requirement>
16 <requirement type="package" >r-blob</requirement> 11 <requirement type="package" >r-blob</requirement>
34 <requirement type="package" version="2.2.1">r-rsqlite</requirement> 29 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
35 <requirement type="package" version="0.2.0">r-dbmodelr</requirement> 30 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
36 --> 31 -->
37 </requirements> 32 </requirements>
38 <stdio> 33 <stdio>
39
40 <exit_code 34 <exit_code
41 range="1" 35 range="1"
42 level="warning" 36 level="warning"
43 description="Selected samples have no data associated to them." 37 description="Selected samples have no data associated to them."
44 /> 38 />
45
46 <exit_code 39 <exit_code
47 range="2" 40 range="2"
48 level="warning" 41 level="warning"
49 description="Some samples have no data associated to them." 42 description="Some samples have no data associated to them."
50 /> 43 />
51
52 </stdio> 44 </stdio>
53
54 <version_command> 45 <version_command>
55 Rscript '$__tool_directory__/XSeekerPreparator.R' -v 46 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
56 </version_command> 47 </version_command>
57
58 <command> 48 <command>
59 <![CDATA[ 49 <![CDATA[
60 Rscript '$__tool_directory__/XSeekerPreparator.R' 50 Rscript '$__tool_directory__/XSeekerPreparator.R'
61
62 -P 51 -P
63
64 --input '$input' 52 --input '$input'
65 --output '$output' 53 --output '$output'
66
67 #if $samples.selected 54 #if $samples.selected
68 --samples '${",".join($samples.selected)}' 55 --samples '${",".join($samples.selected)}'
69 #end if 56 #end if
70
71 #if $database.archetypes 57 #if $database.archetypes
72 --archetype '${",".join($database.archetypes)}' 58 --archetype '${",".join($database.archetypes)}'
73 #end if 59 #end if
74
75 #if $database.base.kind == "tabular" 60 #if $database.base.kind == "tabular"
76 --compounds-csv '${database.base.tabular}' 61 --compounds-csv '${database.base.tabular}'
77 #else if $database.base.kind == "sql" 62 #else if $database.base.kind == "sql"
78 --database '${database.base.sql}' 63 --database '${database.base.sql}'
79 #end if 64 #end if
80
81 #if $database.models.kind == "default" 65 #if $database.models.kind == "default"
82 --models '${base_config}' 66 --models '${base_config}'
83 #else 67 #else
84 --models '${database.models.url}' 68 --models '${database.models.url}'
85 #end if 69 #end if
86 70 #if $class_column
71 --class '${class_column}'
72 #end if
87 ]]> 73 ]]>
88
89 </command> 74 </command>
90
91 <inputs> 75 <inputs>
92 <param 76 <param
93 name="input" 77 name="input"
94 type="data" 78 type="data"
95 multiple="false" 79 multiple="false"
96 label="Rdata to prepare" 80 label="Rdata to prepare"
97 optional="false" 81 optional="false"
98 format="rdata" 82 format="rdata"
83 >
84 </param>
85 <param
86 name="class_column"
87 type="text"
88 value=""
89 label="Column class name"
90 help="
91 The name of the column containing the classes -
92 leave empty to let xsprep guess
93 "
94 optional="true"
99 > 95 >
100 </param> 96 </param>
101 <section name="samples" title="Samples Options" expanded="false"> 97 <section name="samples" title="Samples Options" expanded="false">
102 <param 98 <param
103 name="selected" 99 name="selected"
107 optional="true" 103 optional="true"
108 format="mzml" 104 format="mzml"
109 > 105 >
110 </param> 106 </param>
111 </section> 107 </section>
112
113 <section name="database" title="Database Options" expanded="false"> 108 <section name="database" title="Database Options" expanded="false">
114 <param 109 <param
115 name="archetypes" 110 name="archetypes"
116 type="select" 111 type="select"
117 multiple="true" 112 multiple="true"
118 label="Molecule family (for database's compounds enrichment)" 113 label="Molecule family (for database's compounds enrichment)"
119 > 114 >
120 <option value="G" selected="true">General</option> 115 <option value="G" selected="true">General</option>
121 <option value="H">Halogenates</option> 116 <option value="H">Halogenates</option>
122 </param> 117 </param>
123
124 <conditional name="base"> 118 <conditional name="base">
125 <param name="kind" type="select" label="File containing compound's type"> 119 <param name="kind" type="select" label="File containing compound's type">
126 <option value="none" selected="true">None (deafult)</option> 120 <option value="none" selected="true">None (deafult)</option>
127 <option value="tabular">tabular</option> 121 <option value="tabular">tabular</option>
128 <option value="sql">sql</option> 122 <option value="sql">sql</option>
148 format="sql" 142 format="sql"
149 > 143 >
150 </param> 144 </param>
151 </when> 145 </when>
152 </conditional> 146 </conditional>
153
154 <conditional name="models"> 147 <conditional name="models">
155 <param name="kind" type="select" label="How is the database's model defined"> 148 <param name="kind" type="select" label="How is the database's model defined">
156 <option value="default" selected="true">Default (regular XSeeker Database)</option> 149 <option value="default" selected="true">Default (regular XSeeker Database)</option>
157 <option value="url">Download model file</option> 150 <option value="url">Download model file</option>
158 <option value="git">Get versionned model file</option> 151 <option value="git">Get versionned model file</option>
164 <param name="url" type="text" format="url" label="Repo URL"/> 157 <param name="url" type="text" format="url" label="Repo URL"/>
165 </when> 158 </when>
166 </conditional> 159 </conditional>
167 </section> 160 </section>
168 </inputs> 161 </inputs>
169
170
171 <outputs> 162 <outputs>
172 <data format="sqlite" name="output" /> 163 <data format="sqlite" name="output" />
173 <!-- <data format="xseeker.sqlite" name="output" /> --> 164 <!-- <data format="xseeker.sqlite" name="output" /> -->
174 </outputs> 165 </outputs>
175
176 <configfiles> 166 <configfiles>
177 <configfile name="base_config"> 167 <configfile name="base_config">
178 tryCatch({ 168 tryCatch({
179 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER")) 169 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
180 }, error=function(e) { 170 }, error=function(e) {
181 stop("Please, install DBModelR before you source this file.") 171 stop("Please, install DBModelR before you source this file.")
182 }) 172 })
183
184 list( 173 list(
185 adduct=DBModelR::ModelDefinition( 174 adduct = DBModelR::ModelDefinition(
186 table="adduct", 175 table = "adduct",
187 fields=list( 176 fields = list(
188 name="TEXT", 177 name = "TEXT",
189 mass="FLOAT", 178 mass = "FLOAT",
190 charge="INTEGER", 179 charge = "INTEGER",
191 multi="INTEGER", 180 multi = "INTEGER",
192 formula_add="TEXT", 181 formula_add = "TEXT",
193 formula_ded="TEXT", 182 formula_ded = "TEXT",
194 sign="TEXT", 183 sign = "TEXT",
195 oidscore="INTEGER", 184 oidscore = "INTEGER",
196 quasi="INTEGER", 185 quasi = "INTEGER",
197 ips="FLOAT" 186 ips = "FLOAT"
198 ) 187 )
199 ), 188 ),
200 cluster=DBModelR::ModelDefinition( 189 cluster = DBModelR::ModelDefinition(
201 table="cluster", 190 table = "cluster",
202 fields=list( 191 fields = list(
203 clusterID="INTEGER", 192 clusterID = "INTEGER",
204 formula="TEXT", 193 formula = "TEXT",
205 annotation="TEXT", 194 annotation = "TEXT",
206 coeff="FLOAT", 195 coeff = "FLOAT",
207 r_squared="FLOAT", 196 r_squared = "FLOAT",
208 charge="INTEGER", 197 charge = "INTEGER",
209 mean_rt="FLOAT", 198 mean_rt = "FLOAT",
210 score="FLOAT", 199 score = "FLOAT",
211 deviation="FLOAT", 200 deviation = "FLOAT",
212 status="TEXT", 201 status = "TEXT",
213 curent_group="INTEGER", 202 # adduct = "TEXT",
214 pc_group="INTEGER", 203 curent_group = "INTEGER",
215 align_group="INTEGER", 204 pc_group = "INTEGER",
216 xcms_group="INTEGER" 205 align_group = "INTEGER",
206 xcms_group = "INTEGER"
217 ), 207 ),
218 one=list("sample", "compound", "adduct") 208 one = list("compound", "adduct"),
219 ), 209 many = list("sample")
220 compound=DBModelR::ModelDefinition( 210 ),
221 table="compound", 211 compound = DBModelR::ModelDefinition(
222 fields=list( 212 table = "compound",
223 name="TEXT", 213 fields = list(
224 common_name="TEXT", 214 name = "TEXT",
225 formula="TEXT", 215 common_name = "TEXT",
226 charge="INTEGER", 216 formula = "TEXT",
227 date="TEXT", 217 charge = "INTEGER",
228 mz="FLOAT" 218 date = "TEXT",
229 ) 219 mz = "FLOAT"
230 ), 220 )
231 feature=DBModelR::ModelDefinition( 221 ),
232 table="feature", 222 feature = DBModelR::ModelDefinition(
233 fields=list( 223 table = "feature",
234 featureID="INTEGER", 224 fields = list(
235 mz="FLOAT", 225 featureID = "INTEGER",
236 mz_min="FLOAT", 226 mz = "FLOAT",
237 mz_max="FLOAT", 227 mz_min = "FLOAT",
238 rt="FLOAT", 228 mz_max = "FLOAT",
239 rt_min="FLOAT", 229 rt = "FLOAT",
240 rt_max="FLOAT", 230 rt_min = "FLOAT",
241 int_o="FLOAT", 231 rt_max = "FLOAT",
242 int_b="FLOAT", 232 int_o = "FLOAT",
243 max_o="FLOAT", 233 int_b = "FLOAT",
244 iso="TEXT", 234 max_o = "FLOAT",
245 abundance="FLOAT" 235 iso = "TEXT",
236 abundance = "FLOAT"
246 ), 237 ),
247 one=list("cluster") 238 one = list("cluster"),
248 ), 239 many = list("sample")
249 instrument=DBModelR::ModelDefinition( 240 ),
250 table="instrument", 241 instrument = DBModelR::ModelDefinition(
251 fields=list( 242 table = "instrument",
252 model="TEXT", 243 fields = list(
253 manufacturer="TEXT", 244 model = "TEXT",
254 analyzer="TEXT", 245 manufacturer = "TEXT",
255 detector_type="TEXT", 246 analyzer = "TEXT",
256 ion_source="TEXT" 247 detector_type = "TEXT",
257 ) 248 ion_source = "TEXT"
258 ), 249 )
259 instrument_config=DBModelR::ModelDefinition( 250 ),
260 table="instrument_config", 251 instrument_config = DBModelR::ModelDefinition(
261 fields=list( 252 table = "instrument_config",
262 resolution="TEXT", 253 fields = list(
263 agc_target="TEXT", 254 resolution = "TEXT",
264 maximum_IT="TEXT", 255 agc_target = "TEXT",
265 number_of_scan_range="TEXT", 256 maximum_IT = "TEXT",
266 scan_range="TEXT", 257 number_of_scan_range = "TEXT",
267 version="TEXT" 258 scan_range = "TEXT",
268 ) 259 version = "TEXT"
269 ), 260 )
270 project=DBModelR::ModelDefinition( 261 ),
271 table="project", 262 project = DBModelR::ModelDefinition(
272 fields=list( 263 table = "project",
273 name="TEXT", 264 fields = list(
274 comment="TEXT" 265 name = "TEXT",
266 comment = "TEXT"
275 ), 267 ),
276 one=list("sample") 268 one = list("sample")
277 ), 269 ),
278 sample=DBModelR::ModelDefinition( 270 sample = DBModelR::ModelDefinition(
279 table="sample", 271 table = "sample",
280 fields=list( 272 fields = list(
281 name="TEXT", 273 name = "TEXT",
282 path="TEXT", 274 path = "TEXT",
283 polarity="TEXT", 275 polarity = "TEXT",
284 kind="TEXT", ## rdata or mxml or enriched_rdata 276 kind = "TEXT", ## rdata or mxml or enriched_rdata
285 raw="BLOB" 277 raw = "BLOB"
286 ), 278 ),
287 one=list( 279 one = list(
288 "peak_picking_parameters", 280 "peak_picking_parameters",
289 "pairing_parameters", 281 "pairing_parameters",
290 "alignmenmt_parameters", 282 "alignmenmt_parameters",
291 "camera_parameters", 283 "camera_parameters",
292 "instrument", 284 "instrument",
293 "instrument_config", 285 "instrument_config",
294 "software", 286 "software",
295 "smol_xcms_set" 287 "smol_xcms_set"
296 ) 288 )
297 ), 289 ),
298 smol_xcms_set=DBModelR::ModelDefinition( 290 smol_xcms_set = DBModelR::ModelDefinition(
299 table="smol_xcms_set", 291 table = "smol_xcms_set",
300 fields=list( 292 fields = list(
301 raw="BLOB" 293 raw = "BLOB"
302 ) 294 )
303 ), 295 ),
304 software=DBModelR::ModelDefinition( 296 software = DBModelR::ModelDefinition(
305 table="software", 297 table = "software",
306 fields=list( 298 fields = list(
307 name="TEXT", 299 name = "TEXT",
308 version="TEXT" 300 version = "TEXT"
309 ) 301 )
310 ), 302 ),
311 peak_picking_parameters=DBModelR::ModelDefinition( 303 peak_picking_parameters = DBModelR::ModelDefinition(
312 table="peak_picking_parameters", 304 table = "peak_picking_parameters",
313 fields=list( 305 fields = list(
314 ppm="FLOAT", 306 ppm = "FLOAT",
315 peakwidth="TEXT", 307 peakwidth = "TEXT",
316 snthresh="TEXT", 308 snthresh = "TEXT",
317 prefilterStep="TEXT", 309 prefilterStep = "TEXT",
318 prefilterLevel="TEXT", 310 prefilterLevel = "TEXT",
319 mzdiff="TEXT", 311 mzdiff = "TEXT",
320 fitgauss="TEXT", 312 fitgauss = "TEXT",
321 noise="TEXT", 313 noise = "TEXT",
322 mzCenterFun="TEXT", 314 mzCenterFun = "TEXT",
323 integrate="INTEGER", 315 integrate = "INTEGER",
324 firstBaselineCheck="TEXT", 316 firstBaselineCheck = "TEXT",
325 snthreshIsoROIs="TEXT", 317 snthreshIsoROIs = "TEXT",
326 maxCharge="INTEGER", 318 maxCharge = "INTEGER",
327 maxIso="INTEGER", 319 maxIso = "INTEGER",
328 mzIntervalExtension="TEXT" 320 mzIntervalExtension = "TEXT"
329 ) 321 )
330 ), 322 ),
331 alignmenmt_parameters=DBModelR::ModelDefinition( 323 alignmenmt_parameters = DBModelR::ModelDefinition(
332 table="alignmenmt_parameters", 324 table = "alignmenmt_parameters",
333 fields=list( 325 fields = list(
334 binSize="TEXT", 326 binSize = "TEXT",
335 centerSample="TEXT", 327 centerSample = "TEXT",
336 response="TEXT", 328 response = "TEXT",
337 distFun="TEXT", 329 distFun = "TEXT",
338 gapInit="TEXT", 330 gapInit = "TEXT",
339 gapExtend="TEXT", 331 gapExtend = "TEXT",
340 factorDiag="TEXT", 332 factorDiag = "TEXT",
341 factorGap="TEXT", 333 factorGap = "TEXT",
342 localAlignment="INTEGER", 334 localAlignment = "INTEGER",
343 initPenalty="TEXT", 335 initPenalty = "TEXT",
344 bw="TEXT", 336 bw = "TEXT",
345 minFraction="TEXT", 337 minFraction = "TEXT",
346 minSamples="TEXT", 338 minSamples = "TEXT",
347 maxFeatures="TEXT" 339 maxFeatures = "TEXT"
348 ) 340 )
349 ) 341 )
350 ) 342 )
351 </configfile> 343 </configfile>
352 </configfiles> 344 </configfiles>