Mercurial > repos > lain > xseeker

comparison resources/galaxy/GIE/tools/LC-MSMS/XSeekerPreparator.xml @ 0:15c9fbefeaf1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
" master branch Updating"
author lain
date Tue, 01 Feb 2022 14:19:30 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:15c9fbefeaf1
1 <tool id="xseeker_pwepawatow"
2 name="XSeeker Preparator"
3 version="1.0.0"
4 profile="20.04"
5 >
6 <description>Prepare RData file from CAMERA to be visualized in XSeeker</description>
7
8 <edam_operations>
9 <edam_operation>operation_1812</edam_operation>
10 <edam_operation>operation_0335</edam_operation>
11 </edam_operations>
12
13 <requirements>
14 <requirement type="set_environment">/home/lpavot/R/bin/Rscript</requirement>
15 <!--
16 <requirement type="package" version="4.0.0">R</requirement>
17 -->
18 </requirements>
19
20 <stdio>
21
22 <exit_code
23 range="1"
24 level="warning"
25 description="Selected samples have no data associated to them."
26 />
27
28 <exit_code
29 range="2"
30 level="warning"
31 description="Some samples have no data associated to them."
32 />
33
34 </stdio>
35
36 <version_command>
37 /home/lpavot/R/bin/Rscript '$__tool_directory__/XSeekerPreparator.R' -v
38 </version_command>
39
40 <command>
41 <![CDATA[
42
43 /home/lpavot/R/bin/Rscript '$__tool_directory__/XSeekerPreparator.R'
44
45 -P
46
47 --input '$input'
48 --output '$output'
49
50 #if $samples.selected
51 --samples '${",".join(samples.selected)}'
52 #end if
53
54 #if $database.archetypes
55 --archetype '${",".join($database.archetypes)}'
56 #end if
57
58 #if $database.base.kind == "tabular"
59 --compounds-csv '${database.base.tabular}'
60 #else if $database.base.kind == "sql"
61 --database '${database.base.sql}'
62 #end if
63
64 #if $database.models.kind == "default"
65 --models '${base_config}'
66 #else
67 --models '${database.models.url}'
68 #end if
69 ]]>
70
71 </command>
72
73 <inputs>
74 <param
75 name="input"
76 type="data"
77 multiple="false"
78 label="Rdata to prepare"
79 optional="false"
80 format="rdata"
81 >
82 </param>
83 <section name="samples" title="Samples Options" expanded="false">
84 <param
85 name="selected"
86 type="data"
87 multiple="true"
88 label="Samples to visualize"
89 optional="true"
90 format="mzml"
91 >
92 </param>
93 </section>
94
95 <section name="database" title="Database Options" expanded="false">
96 <param
97 name="archetypes"
98 type="select"
99 multiple="true"
100 label="Molecule family (for database's compounds enrichment)"
101 >
102 <option value="G" selected="true">General</option>
103 <option value="H">Halogenates</option>
104 </param>
105
106 <conditional name="base">
107 <param name="kind" type="select" label="File containing compound's type">
108 <option value="none" selected="true">None (deafult)</option>
109 <option value="tabular">tabular</option>
110 <option value="sql">sql</option>
111 </param>
112 <when value="tabular">
113 <param
114 name="tabular"
115 type="data"
116 multiple="true"
117 label="Tabular file containing compound to use in XSeeker"
118 optional="true"
119 format="tabular"
120 >
121 </param>
122 </when>
123 <when value="sql">
124 <param
125 name="sql"
126 type="data"
127 multiple="true"
128 label="SQL file containing compound to use in XSeeker"
129 optional="true"
130 format="sql"
131 >
132 </param>
133 </when>
134 </conditional>
135
136 <conditional name="models">
137 <param name="kind" type="select" label="How is the database's model defined">
138 <option value="default" selected="true">Default (regular XSeeker Database)</option>
139 <option value="url">Download model file</option>
140 <option value="git">Get versionned model file</option>
141 </param>
142 <when value="url">
143 <param name="url" type="text" format="url" label="File URL"/>
144 </when>
145 <when value="git">
146 <param name="url" type="text" format="url" label="Repo URL"/>
147 </when>
148 </conditional>
149 </section>
150 </inputs>
151
152
153 <outputs>
154 <data format="xseeker.sqlite" name="output" />
155 </outputs>
156
157 <configfiles>
158 <configfile name="base_config">
159 tryCatch({
160 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
161 }, error=function(e) {
162 stop("Please, install DBModelR before you source this file.")
163 })
164
165 list(
166 adduct=DBModelR::ModelDefinition(
167 table="adduct",
168 fields=list(
169 name="TEXT",
170 mass="FLOAT",
171 charge="INTEGER",
172 multi="INTEGER",
173 formula_add="TEXT",
174 formula_ded="TEXT",
175 sign="TEXT",
176 oidscore="INTEGER",
177 quasi="INTEGER",
178 ips="FLOAT"
179 )
180 ),
181 cluster=DBModelR::ModelDefinition(
182 table="cluster",
183 fields=list(
184 clusterID="INTEGER",
185 formula="TEXT",
186 annotation="TEXT",
187 coeff="FLOAT",
188 r_squared="FLOAT",
189 charge="INTEGER",
190 mean_rt="FLOAT",
191 score="FLOAT",
192 deviation="FLOAT",
193 status="TEXT",
194 adduct="TEXT",
195 curent_group="INTEGER",
196 pc_group="INTEGER",
197 align_group="INTEGER",
198 xcms_group="INTEGER"
199 ),
200 one=list("sample", "compound")
201 ),
202 compound=DBModelR::ModelDefinition(
203 table="compound",
204 fields=list(
205 name="TEXT",
206 common_name="TEXT",
207 formula="TEXT",
208 charge="INTEGER",
209 date="TEXT",
210 mz="FLOAT"
211 )
212 ),
213 feature=DBModelR::ModelDefinition(
214 table="feature",
215 fields=list(
216 featureID="INTEGER",
217 mz="FLOAT",
218 mz_min="FLOAT",
219 mz_max="FLOAT",
220 rt="FLOAT",
221 rt_min="FLOAT",
222 rt_max="FLOAT",
223 int_o="FLOAT",
224 int_b="FLOAT",
225 max_o="FLOAT",
226 iso="TEXT",
227 abundance="FLOAT"
228 ),
229 one=list("cluster")
230 ),
231 instrument=DBModelR::ModelDefinition(
232 table="instrument",
233 fields=list(
234 model="TEXT",
235 manufacturer="TEXT",
236 analyzer="TEXT",
237 detector_type="TEXT",
238 ion_source="TEXT"
239 )
240 ),
241 instrument_config=DBModelR::ModelDefinition(
242 table="instrument_config",
243 fields=list(
244 resolution="TEXT",
245 agc_target="TEXT",
246 maximum_IT="TEXT",
247 number_of_scan_range="TEXT",
248 scan_range="TEXT",
249 version="TEXT"
250 )
251 ),
252 project=DBModelR::ModelDefinition(
253 table="project",
254 fields=list(
255 name="TEXT",
256 comment="TEXT"
257 ),
258 one=list("sample")
259 ),
260 sample=DBModelR::ModelDefinition(
261 table="sample",
262 fields=list(
263 name="TEXT",
264 path="TEXT",
265 polarity="TEXT",
266 kind="TEXT", ## rdata or mxml or enriched_rdata
267 raw="BLOB"
268 ),
269 one=list(
270 "peak_picking_parameters",
271 "pairing_parameters",
272 "alignmenmt_parameters",
273 "camera_parameters",
274 "instrument",
275 "instrument_config",
276 "software",
277 "smol_xcms_set"
278 )
279 ),
280 smol_xcms_set=DBModelR::ModelDefinition(
281 table="smol_xcms_set",
282 fields=list(
283 raw="BLOB"
284 )
285 ),
286 software=DBModelR::ModelDefinition(
287 table="software",
288 fields=list(
289 name="TEXT",
290 version="TEXT"
291 )
292 ),
293 peak_picking_parameters=DBModelR::ModelDefinition(
294 table="peak_picking_parameters",
295 fields=list(
296 ppm="FLOAT",
297 peakwidth="TEXT",
298 snthresh="TEXT",
299 prefilterStep="TEXT",
300 prefilterLevel="TEXT",
301 mzdiff="TEXT",
302 fitgauss="TEXT",
303 noise="TEXT",
304 mzCenterFun="TEXT",
305 integrate="INTEGER",
306 firstBaselineCheck="TEXT",
307 snthreshIsoROIs="TEXT",
308 maxCharge="INTEGER",
309 maxIso="INTEGER",
310 mzIntervalExtension="TEXT"
311 )
312 ),
313 alignmenmt_parameters=DBModelR::ModelDefinition(
314 table="alignmenmt_parameters",
315 fields=list(
316 binSize="TEXT",
317 centerSample="TEXT",
318 response="TEXT",
319 distFun="TEXT",
320 gapInit="TEXT",
321 gapExtend="TEXT",
322 factorDiag="TEXT",
323 factorGap="TEXT",
324 localAlignment="INTEGER",
325 initPenalty="TEXT",
326 bw="TEXT",
327 minFraction="TEXT",
328 minSamples="TEXT",
329 maxFeatures="TEXT"
330 )
331 )
332 )
333 </configfile>
334 </configfiles>
335 </tool>