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comparison galaxy/tools/LC-MSMS/XSeekerPreparator.xml @ 0:1660665c081e draft

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#issue9 branch Updating - - Fxx
author fgiacomoni
date Thu, 19 Nov 2020 14:28:46 +0000
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-1:000000000000 0:1660665c081e
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 <!--
16 <requirement type="package" version="4.0.0">R</requirement>
17 -->
18 <requirement type="package" version="4.0.0">R</requirement>
19 <requirement type="package" version="1.6.6">optparse</requirement>
20 <requirement type="package" version="3.10.2">xcms</requirement>
21 <requirement type="package" version="1.2.1">blob</requirement>
22 <requirement type="package" version="0.9.4">fst</requirement>
23 <requirement type="package" version="1.4.0">stringr</requirement>
24 <requirement type="package">DBModelR</requirement>
25 </requirements>
26
27 <stdio>
28
29 <exit_code
30 range="1"
31 level="warning"
32 description="Selected samples have no data associated to them."
33 />
34
35 <exit_code
36 range="2"
37 level="warning"
38 description="Some samples have no data associated to them."
39 />
40
41 </stdio>
42
43 <version_command>
44 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R' -v
45 </version_command>
46
47 <command>
48 <![CDATA[
49
50 R_SCRIPT_PATH '$__tool_directory__/XSeekerPreparator.R'
51
52 -P
53
54 --input '$input'
55 --output '$output'
56
57 #if $samples.selected
58 --samples '${",".join(samples.selected)}'
59 #end if
60
61 #if $database.archetypes
62 --archetype '${",".join($database.archetypes)}'
63 #end if
64
65 #if $database.base.kind == "tabular"
66 --compounds-csv '${database.base.tabular}'
67 #else if $database.base.kind == "sql"
68 --database '${database.base.sql}'
69 #end if
70
71 #if $database.models.kind == "default"
72 --models '${base_config}'
73 #else
74 --models '${database.models.url}'
75 #end if
76
77 ]]>
78
79 </command>
80
81 <inputs>
82 <param
83 name="input"
84 type="data"
85 multiple="false"
86 label="Rdata to prepare"
87 optional="false"
88 format="rdata"
89 >
90 </param>
91 <section name="samples" title="Samples Options" expanded="false">
92 <param
93 name="selected"
94 type="data"
95 multiple="true"
96 label="Samples to visualize"
97 optional="true"
98 format="mzml"
99 >
100 </param>
101 </section>
102
103 <section name="database" title="Database Options" expanded="false">
104 <param
105 name="archetypes"
106 type="select"
107 multiple="true"
108 label="Molecule family (for database's compounds enrichment)"
109 >
110 <option value="G" selected="true">General</option>
111 <option value="H">Halogenates</option>
112 </param>
113
114 <conditional name="base">
115 <param name="kind" type="select" label="File containing compound's type">
116 <option value="none" selected="true">None (deafult)</option>
117 <option value="tabular">tabular</option>
118 <option value="sql">sql</option>
119 </param>
120 <when value="tabular">
121 <param
122 name="tabular"
123 type="data"
124 multiple="true"
125 label="Tabular file containing compound to use in XSeeker"
126 optional="true"
127 format="tabular"
128 >
129 </param>
130 </when>
131 <when value="sql">
132 <param
133 name="sql"
134 type="data"
135 multiple="true"
136 label="SQL file containing compound to use in XSeeker"
137 optional="true"
138 format="sql"
139 >
140 </param>
141 </when>
142 </conditional>
143
144 <conditional name="models">
145 <param name="kind" type="select" label="How is the database's model defined">
146 <option value="default" selected="true">Default (regular XSeeker Database)</option>
147 <option value="url">Download model file</option>
148 <option value="git">Get versionned model file</option>
149 </param>
150 <when value="url">
151 <param name="url" type="text" format="url" label="File URL"/>
152 </when>
153 <when value="git">
154 <param name="url" type="text" format="url" label="Repo URL"/>
155 </when>
156 </conditional>
157 </section>
158 </inputs>
159
160
161 <outputs>
162 <data format="xseeker.sqlite" name="output" />
163 </outputs>
164
165 <configfiles>
166 <configfile name="base_config">
167 tryCatch({
168 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
169 }, error=function(e) {
170 stop("Please, install DBModelR before you source this file.")
171 })
172
173 list(
174 adduct=DBModelR::ModelDefinition(
175 table="adduct",
176 fields=list(
177 name="TEXT",
178 mass="FLOAT",
179 charge="INTEGER",
180 multi="INTEGER",
181 formula_add="TEXT",
182 formula_ded="TEXT",
183 sign="TEXT",
184 oidscore="INTEGER",
185 quasi="INTEGER",
186 ips="FLOAT"
187 )
188 ),
189 cluster=DBModelR::ModelDefinition(
190 table="cluster",
191 fields=list(
192 clusterID="INTEGER",
193 formula="TEXT",
194 annotation="TEXT",
195 coeff="FLOAT",
196 r_squared="FLOAT",
197 charge="INTEGER",
198 mean_rt="FLOAT",
199 score="FLOAT",
200 deviation="FLOAT",
201 status="TEXT",
202 adduct="TEXT",
203 curent_group="INTEGER",
204 pc_group="INTEGER",
205 align_group="INTEGER",
206 xcms_group="INTEGER"
207 ),
208 one=list("sample", "compound")
209 ),
210 compound=DBModelR::ModelDefinition(
211 table="compound",
212 fields=list(
213 name="TEXT",
214 common_name="TEXT",
215 formula="TEXT",
216 charge="INTEGER",
217 date="TEXT",
218 mz="FLOAT"
219 )
220 ),
221 feature=DBModelR::ModelDefinition(
222 table="feature",
223 fields=list(
224 featureID="INTEGER",
225 mz="FLOAT",
226 mz_min="FLOAT",
227 mz_max="FLOAT",
228 rt="FLOAT",
229 rt_min="FLOAT",
230 rt_max="FLOAT",
231 int_o="FLOAT",
232 int_b="FLOAT",
233 max_o="FLOAT",
234 iso="TEXT",
235 abundance="FLOAT"
236 ),
237 one=list("cluster")
238 ),
239 instrument=DBModelR::ModelDefinition(
240 table="instrument",
241 fields=list(
242 model="TEXT",
243 manufacturer="TEXT",
244 analyzer="TEXT",
245 detector_type="TEXT",
246 ion_source="TEXT"
247 )
248 ),
249 instrument_config=DBModelR::ModelDefinition(
250 table="instrument_config",
251 fields=list(
252 resolution="TEXT",
253 agc_target="TEXT",
254 maximum_IT="TEXT",
255 number_of_scan_range="TEXT",
256 scan_range="TEXT",
257 version="TEXT"
258 )
259 ),
260 project=DBModelR::ModelDefinition(
261 table="project",
262 fields=list(
263 name="TEXT",
264 comment="TEXT"
265 ),
266 one=list("sample")
267 ),
268 sample=DBModelR::ModelDefinition(
269 table="sample",
270 fields=list(
271 name="TEXT",
272 path="TEXT",
273 polarity="TEXT",
274 kind="TEXT", ## rdata or mxml or enriched_rdata
275 raw="BLOB"
276 ),
277 one=list(
278 "peak_picking_parameters",
279 "pairing_parameters",
280 "alignmenmt_parameters",
281 "camera_parameters",
282 "instrument",
283 "instrument_config",
284 "software",
285 "smol_xcms_set"
286 )
287 ),
288 smol_xcms_set=DBModelR::ModelDefinition(
289 table="smol_xcms_set",
290 fields=list(
291 raw="BLOB"
292 )
293 ),
294 software=DBModelR::ModelDefinition(
295 table="software",
296 fields=list(
297 name="TEXT",
298 version="TEXT"
299 )
300 ),
301 peak_picking_parameters=DBModelR::ModelDefinition(
302 table="peak_picking_parameters",
303 fields=list(
304 ppm="FLOAT",
305 peakwidth="TEXT",
306 snthresh="TEXT",
307 prefilterStep="TEXT",
308 prefilterLevel="TEXT",
309 mzdiff="TEXT",
310 fitgauss="TEXT",
311 noise="TEXT",
312 mzCenterFun="TEXT",
313 integrate="INTEGER",
314 firstBaselineCheck="TEXT",
315 snthreshIsoROIs="TEXT",
316 maxCharge="INTEGER",
317 maxIso="INTEGER",
318 mzIntervalExtension="TEXT"
319 )
320 ),
321 alignmenmt_parameters=DBModelR::ModelDefinition(
322 table="alignmenmt_parameters",
323 fields=list(
324 binSize="TEXT",
325 centerSample="TEXT",
326 response="TEXT",
327 distFun="TEXT",
328 gapInit="TEXT",
329 gapExtend="TEXT",
330 factorDiag="TEXT",
331 factorGap="TEXT",
332 localAlignment="INTEGER",
333 initPenalty="TEXT",
334 bw="TEXT",
335 minFraction="TEXT",
336 minSamples="TEXT",
337 maxFeatures="TEXT"
338 )
339 )
340 )
341 </configfile>
342 </configfiles>
343 </tool>