Mercurial > repos > lain > xseekerpreparator

comparison XSeekerPreparator.xml @ 2:eb7756ab1cbd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
" master branch Updating"
author lain
date Wed, 25 Nov 2020 13:23:08 +0000
parents
children fa97d16330be
comparison
equal deleted inserted replaced
1:1c2ce385b84e 2:eb7756ab1cbd
1 <tool id="xseeker_preparator"
2 name="XSeeker Preparator"
3 version="1.0.1"
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">R_SCRIPT_PATH</requirement>
15 <requirement type="package" version="4.0.0">R</requirement>
16 <requirement type="package" version="1.6.6">optparse</requirement>
17 <requirement type="package" version="3.10.2">xcms</requirement>
18 <requirement type="package" version="1.2.1">blob</requirement>
19 <requirement type="package" version="0.9.4">fst</requirement>
20 <requirement type="package" version="1.4.0">stringr</requirement>
21 <requirement type="package">DBModelR</requirement>
22 </requirements>
23
24 <stdio>
25
26 <exit_code
27 range="1"
28 level="warning"
29 description="Selected samples have no data associated to them."
30 />
31
32 <exit_code
33 range="2"
34 level="warning"
35 description="Some samples have no data associated to them."
36 />
37
38 </stdio>
39
40 <version_command>
41 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
42 </version_command>
43
44 <command>
45 <![CDATA[
46
47 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
48
49 -P
50
51 --input '$input'
52 --output '$output'
53
54 #if $samples.selected
55 --samples '${",".join(samples.selected)}'
56 #end if
57
58 #if $database.archetypes
59 --archetype '${",".join($database.archetypes)}'
60 #end if
61
62 #if $database.base.kind == "tabular"
63 --compounds-csv '${database.base.tabular}'
64 #else if $database.base.kind == "sql"
65 --database '${database.base.sql}'
66 #end if
67
68 #if $database.models.kind == "default"
69 --models '${base_config}'
70 #else
71 --models '${database.models.url}'
72 #end if
73
74 ]]>
75
76 </command>
77
78 <inputs>
79 <param
80 name="input"
81 type="data"
82 multiple="false"
83 label="Rdata to prepare"
84 optional="false"
85 format="rdata"
86 >
87 </param>
88 <section name="samples" title="Samples Options" expanded="false">
89 <param
90 name="selected"
91 type="data"
92 multiple="true"
93 label="Samples to visualize"
94 optional="true"
95 format="mzml"
96 >
97 </param>
98 </section>
99
100 <section name="database" title="Database Options" expanded="false">
101 <param
102 name="archetypes"
103 type="select"
104 multiple="true"
105 label="Molecule family (for database's compounds enrichment)"
106 >
107 <option value="G" selected="true">General</option>
108 <option value="H">Halogenates</option>
109 </param>
110
111 <conditional name="base">
112 <param name="kind" type="select" label="File containing compound's type">
113 <option value="none" selected="true">None (deafult)</option>
114 <option value="tabular">tabular</option>
115 <option value="sql">sql</option>
116 </param>
117 <when value="tabular">
118 <param
119 name="tabular"
120 type="data"
121 multiple="true"
122 label="Tabular file containing compound to use in XSeeker"
123 optional="true"
124 format="tabular"
125 >
126 </param>
127 </when>
128 <when value="sql">
129 <param
130 name="sql"
131 type="data"
132 multiple="true"
133 label="SQL file containing compound to use in XSeeker"
134 optional="true"
135 format="sql"
136 >
137 </param>
138 </when>
139 </conditional>
140
141 <conditional name="models">
142 <param name="kind" type="select" label="How is the database's model defined">
143 <option value="default" selected="true">Default (regular XSeeker Database)</option>
144 <option value="url">Download model file</option>
145 <option value="git">Get versionned model file</option>
146 </param>
147 <when value="url">
148 <param name="url" type="text" format="url" label="File URL"/>
149 </when>
150 <when value="git">
151 <param name="url" type="text" format="url" label="Repo URL"/>
152 </when>
153 </conditional>
154 </section>
155 </inputs>
156
157
158 <outputs>
159 <data format="xseeker.sqlite" name="output" />
160 </outputs>
161
162 <configfiles>
163 <configfile name="base_config">
164 tryCatch({
165 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
166 }, error=function(e) {
167 stop("Please, install DBModelR before you source this file.")
168 })
169
170 list(
171 adduct=DBModelR::ModelDefinition(
172 table="adduct",
173 fields=list(
174 name="TEXT",
175 mass="FLOAT",
176 charge="INTEGER",
177 multi="INTEGER",
178 formula_add="TEXT",
179 formula_ded="TEXT",
180 sign="TEXT",
181 oidscore="INTEGER",
182 quasi="INTEGER",
183 ips="FLOAT"
184 )
185 ),
186 cluster=DBModelR::ModelDefinition(
187 table="cluster",
188 fields=list(
189 clusterID="INTEGER",
190 formula="TEXT",
191 annotation="TEXT",
192 coeff="FLOAT",
193 r_squared="FLOAT",
194 charge="INTEGER",
195 mean_rt="FLOAT",
196 score="FLOAT",
197 deviation="FLOAT",
198 status="TEXT",
199 adduct="TEXT",
200 curent_group="INTEGER",
201 pc_group="INTEGER",
202 align_group="INTEGER",
203 xcms_group="INTEGER"
204 ),
205 one=list("sample", "compound")
206 ),
207 compound=DBModelR::ModelDefinition(
208 table="compound",
209 fields=list(
210 name="TEXT",
211 common_name="TEXT",
212 formula="TEXT",
213 charge="INTEGER",
214 date="TEXT",
215 mz="FLOAT"
216 )
217 ),
218 feature=DBModelR::ModelDefinition(
219 table="feature",
220 fields=list(
221 featureID="INTEGER",
222 mz="FLOAT",
223 mz_min="FLOAT",
224 mz_max="FLOAT",
225 rt="FLOAT",
226 rt_min="FLOAT",
227 rt_max="FLOAT",
228 int_o="FLOAT",
229 int_b="FLOAT",
230 max_o="FLOAT",
231 iso="TEXT",
232 abundance="FLOAT"
233 ),
234 one=list("cluster")
235 ),
236 instrument=DBModelR::ModelDefinition(
237 table="instrument",
238 fields=list(
239 model="TEXT",
240 manufacturer="TEXT",
241 analyzer="TEXT",
242 detector_type="TEXT",
243 ion_source="TEXT"
244 )
245 ),
246 instrument_config=DBModelR::ModelDefinition(
247 table="instrument_config",
248 fields=list(
249 resolution="TEXT",
250 agc_target="TEXT",
251 maximum_IT="TEXT",
252 number_of_scan_range="TEXT",
253 scan_range="TEXT",
254 version="TEXT"
255 )
256 ),
257 project=DBModelR::ModelDefinition(
258 table="project",
259 fields=list(
260 name="TEXT",
261 comment="TEXT"
262 ),
263 one=list("sample")
264 ),
265 sample=DBModelR::ModelDefinition(
266 table="sample",
267 fields=list(
268 name="TEXT",
269 path="TEXT",
270 polarity="TEXT",
271 kind="TEXT", ## rdata or mxml or enriched_rdata
272 raw="BLOB"
273 ),
274 one=list(
275 "peak_picking_parameters",
276 "pairing_parameters",
277 "alignmenmt_parameters",
278 "camera_parameters",
279 "instrument",
280 "instrument_config",
281 "software",
282 "smol_xcms_set"
283 )
284 ),
285 smol_xcms_set=DBModelR::ModelDefinition(
286 table="smol_xcms_set",
287 fields=list(
288 raw="BLOB"
289 )
290 ),
291 software=DBModelR::ModelDefinition(
292 table="software",
293 fields=list(
294 name="TEXT",
295 version="TEXT"
296 )
297 ),
298 peak_picking_parameters=DBModelR::ModelDefinition(
299 table="peak_picking_parameters",
300 fields=list(
301 ppm="FLOAT",
302 peakwidth="TEXT",
303 snthresh="TEXT",
304 prefilterStep="TEXT",
305 prefilterLevel="TEXT",
306 mzdiff="TEXT",
307 fitgauss="TEXT",
308 noise="TEXT",
309 mzCenterFun="TEXT",
310 integrate="INTEGER",
311 firstBaselineCheck="TEXT",
312 snthreshIsoROIs="TEXT",
313 maxCharge="INTEGER",
314 maxIso="INTEGER",
315 mzIntervalExtension="TEXT"
316 )
317 ),
318 alignmenmt_parameters=DBModelR::ModelDefinition(
319 table="alignmenmt_parameters",
320 fields=list(
321 binSize="TEXT",
322 centerSample="TEXT",
323 response="TEXT",
324 distFun="TEXT",
325 gapInit="TEXT",
326 gapExtend="TEXT",
327 factorDiag="TEXT",
328 factorGap="TEXT",
329 localAlignment="INTEGER",
330 initPenalty="TEXT",
331 bw="TEXT",
332 minFraction="TEXT",
333 minSamples="TEXT",
334 maxFeatures="TEXT"
335 )
336 )
337 )
338 </configfile>
339 </configfiles>
340 </tool>