|
2
|
1 <tool id="xseeker_preparator"
|
|
0
|
2 name="XSeeker Preparator"
|
|
16
|
3 version="1.2.3"
|
|
0
|
4 >
|
|
|
5 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
|
|
|
6
|
|
|
7 <edam_operations>
|
|
|
8 <edam_operation>operation_1812</edam_operation>
|
|
|
9 <edam_operation>operation_0335</edam_operation>
|
|
|
10 </edam_operations>
|
|
|
11
|
|
|
12 <requirements>
|
|
16
|
13 <requirement type="package" >bioconductor-xcms</requirement>
|
|
|
14 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
|
|
|
15 <requirement type="package" >git</requirement>
|
|
|
16 <requirement type="package" >r-blob</requirement>
|
|
|
17 <requirement type="package" >r-dbi</requirement>
|
|
|
18 <requirement type="package" >r-fst</requirement>
|
|
|
19 <requirement type="package" >r-optparse</requirement>
|
|
|
20 <requirement type="package" >r-stringr</requirement>
|
|
|
21 <requirement type="package" >r-purrr</requirement>
|
|
|
22 <requirement type="package" >r-rsqlite</requirement>
|
|
|
23 <requirement type="package" >r-dbmodelr</requirement>
|
|
|
24 <!--
|
|
4
|
25 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
|
|
15
|
26 <requirement type="package" version="1.48.0">bioconductor-camera</requirement>
|
|
14
|
27 <requirement type="package" version="2.29.2">git</requirement>
|
|
4
|
28 <requirement type="package" version="1.2.1">r-blob</requirement>
|
|
|
29 <requirement type="package" version="1.1.0">r-dbi</requirement>
|
|
|
30 <requirement type="package" version="0.9.4">r-fst</requirement>
|
|
|
31 <requirement type="package" version="1.6.6">r-optparse</requirement>
|
|
|
32 <requirement type="package" version="1.4.0">r-stringr</requirement>
|
|
|
33 <requirement type="package" version="0.3.4">r-purrr</requirement>
|
|
|
34 <requirement type="package" version="2.2.1">r-rsqlite</requirement>
|
|
14
|
35 <requirement type="package" version="0.2.0">r-dbmodelr</requirement>
|
|
16
|
36 -->
|
|
0
|
37 </requirements>
|
|
|
38 <stdio>
|
|
|
39
|
|
|
40 <exit_code
|
|
|
41 range="1"
|
|
|
42 level="warning"
|
|
|
43 description="Selected samples have no data associated to them."
|
|
|
44 />
|
|
|
45
|
|
|
46 <exit_code
|
|
|
47 range="2"
|
|
|
48 level="warning"
|
|
|
49 description="Some samples have no data associated to them."
|
|
|
50 />
|
|
|
51
|
|
|
52 </stdio>
|
|
|
53
|
|
|
54 <version_command>
|
|
4
|
55 Rscript '$__tool_directory__/XSeekerPreparator.R' -v
|
|
0
|
56 </version_command>
|
|
|
57
|
|
|
58 <command>
|
|
|
59 <![CDATA[
|
|
4
|
60 Rscript '$__tool_directory__/XSeekerPreparator.R'
|
|
0
|
61
|
|
|
62 -P
|
|
|
63
|
|
|
64 --input '$input'
|
|
|
65 --output '$output'
|
|
|
66
|
|
|
67 #if $samples.selected
|
|
4
|
68 --samples '${",".join($samples.selected)}'
|
|
0
|
69 #end if
|
|
|
70
|
|
|
71 #if $database.archetypes
|
|
|
72 --archetype '${",".join($database.archetypes)}'
|
|
|
73 #end if
|
|
|
74
|
|
|
75 #if $database.base.kind == "tabular"
|
|
|
76 --compounds-csv '${database.base.tabular}'
|
|
|
77 #else if $database.base.kind == "sql"
|
|
|
78 --database '${database.base.sql}'
|
|
|
79 #end if
|
|
|
80
|
|
|
81 #if $database.models.kind == "default"
|
|
|
82 --models '${base_config}'
|
|
|
83 #else
|
|
|
84 --models '${database.models.url}'
|
|
|
85 #end if
|
|
|
86
|
|
|
87 ]]>
|
|
|
88
|
|
|
89 </command>
|
|
|
90
|
|
|
91 <inputs>
|
|
|
92 <param
|
|
|
93 name="input"
|
|
|
94 type="data"
|
|
|
95 multiple="false"
|
|
|
96 label="Rdata to prepare"
|
|
|
97 optional="false"
|
|
|
98 format="rdata"
|
|
|
99 >
|
|
|
100 </param>
|
|
|
101 <section name="samples" title="Samples Options" expanded="false">
|
|
|
102 <param
|
|
|
103 name="selected"
|
|
|
104 type="data"
|
|
|
105 multiple="true"
|
|
|
106 label="Samples to visualize"
|
|
|
107 optional="true"
|
|
|
108 format="mzml"
|
|
|
109 >
|
|
|
110 </param>
|
|
|
111 </section>
|
|
|
112
|
|
|
113 <section name="database" title="Database Options" expanded="false">
|
|
|
114 <param
|
|
|
115 name="archetypes"
|
|
|
116 type="select"
|
|
|
117 multiple="true"
|
|
|
118 label="Molecule family (for database's compounds enrichment)"
|
|
|
119 >
|
|
|
120 <option value="G" selected="true">General</option>
|
|
|
121 <option value="H">Halogenates</option>
|
|
|
122 </param>
|
|
|
123
|
|
|
124 <conditional name="base">
|
|
|
125 <param name="kind" type="select" label="File containing compound's type">
|
|
|
126 <option value="none" selected="true">None (deafult)</option>
|
|
|
127 <option value="tabular">tabular</option>
|
|
|
128 <option value="sql">sql</option>
|
|
|
129 </param>
|
|
|
130 <when value="tabular">
|
|
|
131 <param
|
|
|
132 name="tabular"
|
|
|
133 type="data"
|
|
|
134 multiple="true"
|
|
|
135 label="Tabular file containing compound to use in XSeeker"
|
|
|
136 optional="true"
|
|
|
137 format="tabular"
|
|
|
138 >
|
|
|
139 </param>
|
|
|
140 </when>
|
|
|
141 <when value="sql">
|
|
|
142 <param
|
|
|
143 name="sql"
|
|
|
144 type="data"
|
|
|
145 multiple="true"
|
|
|
146 label="SQL file containing compound to use in XSeeker"
|
|
|
147 optional="true"
|
|
|
148 format="sql"
|
|
|
149 >
|
|
|
150 </param>
|
|
|
151 </when>
|
|
|
152 </conditional>
|
|
|
153
|
|
|
154 <conditional name="models">
|
|
|
155 <param name="kind" type="select" label="How is the database's model defined">
|
|
|
156 <option value="default" selected="true">Default (regular XSeeker Database)</option>
|
|
|
157 <option value="url">Download model file</option>
|
|
|
158 <option value="git">Get versionned model file</option>
|
|
|
159 </param>
|
|
|
160 <when value="url">
|
|
|
161 <param name="url" type="text" format="url" label="File URL"/>
|
|
|
162 </when>
|
|
|
163 <when value="git">
|
|
|
164 <param name="url" type="text" format="url" label="Repo URL"/>
|
|
|
165 </when>
|
|
|
166 </conditional>
|
|
|
167 </section>
|
|
|
168 </inputs>
|
|
|
169
|
|
|
170
|
|
|
171 <outputs>
|
|
3
|
172 <data format="sqlite" name="output" />
|
|
4
|
173 <!-- <data format="xseeker.sqlite" name="output" /> -->
|
|
0
|
174 </outputs>
|
|
|
175
|
|
|
176 <configfiles>
|
|
|
177 <configfile name="base_config">
|
|
|
178 tryCatch({
|
|
|
179 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
|
|
|
180 }, error=function(e) {
|
|
|
181 stop("Please, install DBModelR before you source this file.")
|
|
|
182 })
|
|
|
183
|
|
|
184 list(
|
|
|
185 adduct=DBModelR::ModelDefinition(
|
|
|
186 table="adduct",
|
|
|
187 fields=list(
|
|
|
188 name="TEXT",
|
|
|
189 mass="FLOAT",
|
|
|
190 charge="INTEGER",
|
|
|
191 multi="INTEGER",
|
|
|
192 formula_add="TEXT",
|
|
|
193 formula_ded="TEXT",
|
|
|
194 sign="TEXT",
|
|
|
195 oidscore="INTEGER",
|
|
|
196 quasi="INTEGER",
|
|
|
197 ips="FLOAT"
|
|
|
198 )
|
|
|
199 ),
|
|
|
200 cluster=DBModelR::ModelDefinition(
|
|
|
201 table="cluster",
|
|
|
202 fields=list(
|
|
|
203 clusterID="INTEGER",
|
|
|
204 formula="TEXT",
|
|
|
205 annotation="TEXT",
|
|
|
206 coeff="FLOAT",
|
|
|
207 r_squared="FLOAT",
|
|
|
208 charge="INTEGER",
|
|
|
209 mean_rt="FLOAT",
|
|
|
210 score="FLOAT",
|
|
|
211 deviation="FLOAT",
|
|
|
212 status="TEXT",
|
|
|
213 curent_group="INTEGER",
|
|
|
214 pc_group="INTEGER",
|
|
|
215 align_group="INTEGER",
|
|
|
216 xcms_group="INTEGER"
|
|
|
217 ),
|
|
12
|
218 one=list("sample", "compound", "adduct")
|
|
0
|
219 ),
|
|
|
220 compound=DBModelR::ModelDefinition(
|
|
|
221 table="compound",
|
|
|
222 fields=list(
|
|
|
223 name="TEXT",
|
|
|
224 common_name="TEXT",
|
|
|
225 formula="TEXT",
|
|
|
226 charge="INTEGER",
|
|
|
227 date="TEXT",
|
|
|
228 mz="FLOAT"
|
|
|
229 )
|
|
|
230 ),
|
|
|
231 feature=DBModelR::ModelDefinition(
|
|
|
232 table="feature",
|
|
|
233 fields=list(
|
|
|
234 featureID="INTEGER",
|
|
|
235 mz="FLOAT",
|
|
|
236 mz_min="FLOAT",
|
|
|
237 mz_max="FLOAT",
|
|
|
238 rt="FLOAT",
|
|
|
239 rt_min="FLOAT",
|
|
|
240 rt_max="FLOAT",
|
|
|
241 int_o="FLOAT",
|
|
|
242 int_b="FLOAT",
|
|
|
243 max_o="FLOAT",
|
|
|
244 iso="TEXT",
|
|
|
245 abundance="FLOAT"
|
|
|
246 ),
|
|
|
247 one=list("cluster")
|
|
|
248 ),
|
|
|
249 instrument=DBModelR::ModelDefinition(
|
|
|
250 table="instrument",
|
|
|
251 fields=list(
|
|
|
252 model="TEXT",
|
|
|
253 manufacturer="TEXT",
|
|
|
254 analyzer="TEXT",
|
|
|
255 detector_type="TEXT",
|
|
|
256 ion_source="TEXT"
|
|
|
257 )
|
|
|
258 ),
|
|
|
259 instrument_config=DBModelR::ModelDefinition(
|
|
|
260 table="instrument_config",
|
|
|
261 fields=list(
|
|
|
262 resolution="TEXT",
|
|
|
263 agc_target="TEXT",
|
|
|
264 maximum_IT="TEXT",
|
|
|
265 number_of_scan_range="TEXT",
|
|
|
266 scan_range="TEXT",
|
|
|
267 version="TEXT"
|
|
|
268 )
|
|
|
269 ),
|
|
|
270 project=DBModelR::ModelDefinition(
|
|
|
271 table="project",
|
|
|
272 fields=list(
|
|
|
273 name="TEXT",
|
|
|
274 comment="TEXT"
|
|
|
275 ),
|
|
|
276 one=list("sample")
|
|
|
277 ),
|
|
|
278 sample=DBModelR::ModelDefinition(
|
|
|
279 table="sample",
|
|
|
280 fields=list(
|
|
|
281 name="TEXT",
|
|
|
282 path="TEXT",
|
|
|
283 polarity="TEXT",
|
|
|
284 kind="TEXT", ## rdata or mxml or enriched_rdata
|
|
|
285 raw="BLOB"
|
|
|
286 ),
|
|
|
287 one=list(
|
|
|
288 "peak_picking_parameters",
|
|
|
289 "pairing_parameters",
|
|
|
290 "alignmenmt_parameters",
|
|
|
291 "camera_parameters",
|
|
|
292 "instrument",
|
|
|
293 "instrument_config",
|
|
|
294 "software",
|
|
|
295 "smol_xcms_set"
|
|
|
296 )
|
|
|
297 ),
|
|
|
298 smol_xcms_set=DBModelR::ModelDefinition(
|
|
|
299 table="smol_xcms_set",
|
|
|
300 fields=list(
|
|
|
301 raw="BLOB"
|
|
|
302 )
|
|
|
303 ),
|
|
|
304 software=DBModelR::ModelDefinition(
|
|
|
305 table="software",
|
|
|
306 fields=list(
|
|
|
307 name="TEXT",
|
|
|
308 version="TEXT"
|
|
|
309 )
|
|
|
310 ),
|
|
|
311 peak_picking_parameters=DBModelR::ModelDefinition(
|
|
|
312 table="peak_picking_parameters",
|
|
|
313 fields=list(
|
|
|
314 ppm="FLOAT",
|
|
|
315 peakwidth="TEXT",
|
|
|
316 snthresh="TEXT",
|
|
|
317 prefilterStep="TEXT",
|
|
|
318 prefilterLevel="TEXT",
|
|
|
319 mzdiff="TEXT",
|
|
|
320 fitgauss="TEXT",
|
|
|
321 noise="TEXT",
|
|
|
322 mzCenterFun="TEXT",
|
|
|
323 integrate="INTEGER",
|
|
|
324 firstBaselineCheck="TEXT",
|
|
|
325 snthreshIsoROIs="TEXT",
|
|
|
326 maxCharge="INTEGER",
|
|
|
327 maxIso="INTEGER",
|
|
|
328 mzIntervalExtension="TEXT"
|
|
|
329 )
|
|
|
330 ),
|
|
|
331 alignmenmt_parameters=DBModelR::ModelDefinition(
|
|
|
332 table="alignmenmt_parameters",
|
|
|
333 fields=list(
|
|
|
334 binSize="TEXT",
|
|
|
335 centerSample="TEXT",
|
|
|
336 response="TEXT",
|
|
|
337 distFun="TEXT",
|
|
|
338 gapInit="TEXT",
|
|
|
339 gapExtend="TEXT",
|
|
|
340 factorDiag="TEXT",
|
|
|
341 factorGap="TEXT",
|
|
|
342 localAlignment="INTEGER",
|
|
|
343 initPenalty="TEXT",
|
|
|
344 bw="TEXT",
|
|
|
345 minFraction="TEXT",
|
|
|
346 minSamples="TEXT",
|
|
|
347 maxFeatures="TEXT"
|
|
|
348 )
|
|
|
349 )
|
|
|
350 )
|
|
|
351 </configfile>
|
|
|
352 </configfiles>
|
|
|
353 </tool>
|
