Mercurial > repos > fgiacomoni > bank_inhouse
comparison bank_inhouse.xml @ 0:be582bcd6585 draft
Master branch Updating - - Fxx
author | fgiacomoni |
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date | Thu, 04 Oct 2018 10:37:14 -0400 |
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children | 52798007c6b2 |
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1 <tool id="bank_inhouse" name="bank_inhouse" version="1.1.3"> | |
2 <description> | |
3 search by accurate mass (and by Retention time) on a local bank | |
4 </description> | |
5 | |
6 <requirements> | |
7 <requirement type="package" version="2.90">perl-json</requirement> | |
8 <requirement type="package" version="1.97">perl-text-csv</requirement> | |
9 <requirement type="package" version="6.15">perl-lwp-simple</requirement> | |
10 <requirement type="package" version="1.74">perl-uri</requirement> | |
11 <requirement type="package" version="1.19">perl-soap-lite</requirement> | |
12 <requirement type="package" version="2.97">perl-html-template</requirement> | |
13 <requirement type="package" version="0.428">perl-list-moreutils</requirement> | |
14 <requirement type="package" version="6.15">perl-libwww-perl</requirement> | |
15 </requirements> | |
16 <stdio> | |
17 <exit_code range="1" level="fatal" /> | |
18 </stdio> | |
19 | |
20 <command><![CDATA[ | |
21 perl $__tool_directory__/bank_inhouse.pl | |
22 | |
23 #if str($input_type.choice) == "YES": | |
24 -input "${input_type.variableMetadata_in}" | |
25 #if str($input_type.header.header_choice) == "YES": | |
26 -nbheader "${input_type.header.nbheader}" | |
27 #end if | |
28 | |
29 -colmass "${input_type.colmass}" | |
30 #if str($input_type.use_file_rt.rt_file_choice) == "YES": | |
31 -colrt "${input_type.use_file_rt.colrt}" | |
32 -rt_delta "${input_type.use_file_rt.rt_file_delta}" | |
33 #end if | |
34 #else: | |
35 #if str($input_type.use_rt.rt_choice) == "YES": | |
36 -rt "${input_type.use_rt.rt}" | |
37 -rt_delta "${input_type.use_rt.rt_delta}" | |
38 #end if | |
39 -masse "${input_type.masse}" | |
40 #end if | |
41 | |
42 -mz_delta "${mz_delta_type.mz_delta}" | |
43 -mass_delta "${mz_delta_type.mass_delta}" | |
44 | |
45 #if str($bank_type.perso_bank) == "YES": | |
46 -bank_in "${bank_type.bank_in}" -bank_name "${bank_type.bank_in.name}" | |
47 -mzdb "${bank_type.mzdb}" | |
48 #if str($bank_type.bank_rt.bank_rt_choice) == "YES": | |
49 -rtdb "${bank_type.bank_rt.rtdb}" | |
50 #end if | |
51 #end if | |
52 | |
53 #if str($input_type.choice) == "YES": | |
54 -outputTab "$variableMetadata_out" | |
55 -outputXls "$bankInhouseResXls_filein" | |
56 #if str($outfiles) == "YES": | |
57 -outputFull "$variableMetadata_full_out" | |
58 #end if | |
59 #else: | |
60 -outputXls "$bankInhouseResXls_manualin" | |
61 #end if | |
62 | |
63 #if str($outfiles) == "YES": | |
64 -outputJson "$Json" | |
65 #end if | |
66 ]]></command> | |
67 | |
68 <inputs> | |
69 <conditional name="input_type"> | |
70 <param name="choice" type="select" display="radio" label="* Would you use a file?" help="if 'NO' is selected then one or more mass(es) must be entered manually"> | |
71 <option value="NO">NO</option> | |
72 <option value="YES" selected="true">YES</option> | |
73 </param> | |
74 <when value="YES"> | |
75 <param name="variableMetadata_in" type="data" label="FILE OF MASSES (format: tabular)" help="Generally variable metadata file" format="tabular" /> | |
76 | |
77 <conditional name="header"> | |
78 <param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" /> | |
79 <when value="YES"> | |
80 <param name="nbheader" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/> | |
81 </when> | |
82 <when value="NO"/> | |
83 </conditional> | |
84 | |
85 <conditional name="use_file_rt"> | |
86 <param name="rt_file_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? In your analyzed file? Would you use it?" /> | |
87 <when value="YES"> | |
88 <param name="colrt" label="Column of retention time (RT)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> | |
89 <param name="rt_file_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/> | |
90 </when> | |
91 <when value="NO"/> | |
92 </conditional> | |
93 | |
94 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> | |
95 </when> | |
96 <when value="NO"> | |
97 <conditional name="use_rt"> | |
98 <param name="rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? Would you use it?" /> | |
99 <when value="YES"> | |
100 <param name="rt" label="retention time (RT) to submit" type="text" size="10" help="For a rt list, writes : rt1 rt2 rt3. Your values must be separated by spaces. You should use dot (.) like decimal separator"/> | |
101 <param name="rt_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/> | |
102 </when> | |
103 <when value="NO"/> | |
104 </conditional> | |
105 | |
106 <param name="masse" type="text" label="Mass (MZ) to submit" size="20" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator"/> | |
107 </when> | |
108 </conditional> | |
109 | |
110 <conditional name="mz_delta_type"> | |
111 <param name="mz_delta" label="Delta type" type="select" display="radio" help=""> | |
112 <option value="Da">Da</option> | |
113 <option value="ppm">ppm</option> | |
114 </param> | |
115 <when value="Da"> | |
116 <param name="mass_delta" label="Delta of mass (MZ) (in Dalton)" type="float" value="0.005" min="0" max="3000" help="Default value is 0.005 Da"/> | |
117 </when> | |
118 <when value="ppm"> | |
119 <param name="mass_delta" label="Delta of mass (MZ) (in ppm)" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/> | |
120 </when> | |
121 </conditional> | |
122 | |
123 <conditional name="bank_type"> | |
124 <param name="perso_bank" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="* Use personal data bank?" help="if 'NO' is selected an internal file will be used! It doesn't contain a retention time (RT)" /> | |
125 <when value="YES"> | |
126 <param name="bank_in" type="data" label="BANK FILE" help="" format="tabular" /> | |
127 <param name="mzdb" label="Column of masses (MZ) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" /> | |
128 <conditional name="bank_rt"> | |
129 <param name="bank_rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Have you used the retention time (RT) for your input data?" help="Do you have retention times in your bank? In your analyzed data? Would you use it?" /> | |
130 <when value="YES"> | |
131 <param name="rtdb" label="Column of retention time (RT) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" /> | |
132 </when> | |
133 <when value="NO"/> | |
134 </conditional> | |
135 </when> | |
136 <when value="NO"/> | |
137 </conditional> | |
138 <param name="outfiles" type="select" label="* Would you more output?" display="radio" help="if 'YES' is selected then 2 more files will be generate (JSON + variableMetadata and bank full column)"> | |
139 <option value="YES">YES</option> | |
140 <option value="NO" selected="true">NO</option> | |
141 </param> | |
142 </inputs> | |
143 | |
144 <outputs> | |
145 <data name="variableMetadata_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_TSV" > | |
146 <filter>(input_type['choice'] == 'YES')</filter> | |
147 </data> | |
148 <data name="bankInhouseResXls_filein" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_XLS" > | |
149 <filter>(input_type['choice'] == 'YES')</filter> | |
150 </data> | |
151 <data name="variableMetadata_full_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_full_TSV" > | |
152 <filter>(input_type['choice'] == 'YES')</filter> | |
153 <filter>(outfiles == 'YES')</filter> | |
154 </data> | |
155 <data name="bankInhouseResXls_manualin" format="tabular" label="${tool.name}_manual_XLS" > | |
156 <filter>(input_type['choice'] == 'NO')</filter> | |
157 </data> | |
158 <data name="Json" format="vjson" label="${tool.name}_Json" > | |
159 <filter>(outfiles == 'YES')</filter> | |
160 </data> | |
161 <!--<data name="View" format="html" label="${tool.name}_View" ></data>--> | |
162 </outputs> | |
163 | |
164 <tests> | |
165 <test> | |
166 <param name="choice" value="NO"/> | |
167 <param name="rt_choice" value="NO"/> | |
168 <param name="masse" value="422.0849114 18.0105647 535.3181236 209.987659 98.952389"/> | |
169 <param name="mz_delta" value="Da"/> | |
170 <param name="mass_delta" value="0.005"/> | |
171 <param name="perso_bank" value="NO"/> | |
172 <param name="outfiles" value="NO"/> | |
173 <output name="bankInhouseResXls_manualin" file="out_test1.tabular"/> | |
174 </test> | |
175 <test> | |
176 <param name="choice" value="YES"/> | |
177 <param name="variableMetadata_in" value="in_test2.tabular"/> | |
178 <param name="header_choice" value="YES"/> | |
179 <param name="nbheader" value="1"/> | |
180 <param name="rt_file_choice" value="NO"/> | |
181 <param name="colmass" value="2"/> | |
182 <param name="mz_delta" value="Da"/> | |
183 <param name="mass_delta" value="0.005"/> | |
184 <param name="perso_bank" value="NO"/> | |
185 <param name="outfiles" value="NO"/> | |
186 | |
187 <output name="variableMetadata_out" file="out_test2a.tabular"/> | |
188 <output name="bankInhouseResXls_filein" file="out_test2b.tabular"/> | |
189 </test> | |
190 <!-- | |
191 <test> | |
192 <param name="choice" value="YES"/> | |
193 <param name="variableMetadata_in" value="in_test3.tabular"/> | |
194 <param name="header_choice" value="YES"/> | |
195 <param name="nbheader" value="1"/> | |
196 <param name="rt_file_choice" value="NO"/> | |
197 <param name="colmass" value="2"/> | |
198 <param name="mz_delta" value="Da"/> | |
199 <param name="mass_delta" value="0.005"/> | |
200 <param name="perso_bank" value="NO"/> | |
201 <param name="outfiles" value="NO"/> | |
202 | |
203 <output name="variableMetadata_out" file="out_test3a.tabular"/> | |
204 <output name="bankInhouseResXls_filein" file="out_test3b.tabular"/> | |
205 </test> | |
206 <test> | |
207 <param name="choice" value="YES"/> | |
208 <param name="variableMetadata_in" value="in_test4.tabular"/> | |
209 <param name="header_choice" value="YES"/> | |
210 <param name="nbheader" value="1"/> | |
211 <param name="rt_file_choice" value="YES"/> | |
212 <param name="colrt" value="10"/> | |
213 <param name="rt_file_delta" value="0.2"/> | |
214 <param name="colmass" value="8"/> | |
215 <param name="mz_delta" value="Da"/> | |
216 <param name="mass_delta" value="0"/> | |
217 <param name="perso_bank" value="YES"/> | |
218 <param name="bank_in" value="in_test4.tabular"/> | |
219 <param name="mzdb" value="8"/> | |
220 <param name="bank_rt_choice" value="YES"/> | |
221 <param name="rtdb" value="10"/> | |
222 <param name="outfiles" value="YES"/> | |
223 | |
224 <output name="variableMetadata_out" file="out_test4a.tabular"/> | |
225 <output name="bankInhouseResXls_filein" file="out_test4b.tabular"/> | |
226 <output name="variableMetadata_full_out" file="out_test4c.tabular"/> | |
227 <output name="Json" file="out_test4d.vjson"/> | |
228 </test>--> | |
229 </tests> | |
230 | |
231 <help><![CDATA[ | |
232 | |
233 .. class:: infomark | |
234 | |
235 **Authors** | |
236 | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) | |
237 | |
238 --------------------------------------------------- | |
239 | |
240 | |
241 ============== | |
242 bank_inhouse | |
243 ============== | |
244 | |
245 ----------- | |
246 Description | |
247 ----------- | |
248 | |
249 | Search informations on a local bank with one or more mass(es), with or without retention time, in a file or entered manually | |
250 | |
251 | |
252 Keywords | |
253 ======== | |
254 | |
255 Masses + rt to inhouse info | |
256 | |
257 | |
258 ----------------- | |
259 Workflow position | |
260 ----------------- | |
261 | |
262 | |
263 .. image:: bank_inhouse.png | |
264 :width: 800 | |
265 | |
266 | |
267 ----------- | |
268 Input files | |
269 ----------- | |
270 | |
271 | |
272 +-----------------------------+-----------+ | |
273 | Parameter : num + label | Format | | |
274 +=============================+===========+ | |
275 | 1 : File of masses | tabular | | |
276 +-----------------------------+-----------+ | |
277 | 2 : personal data bank file | tabular | | |
278 +-----------------------------+-----------+ | |
279 | |
280 File of masses (Generally variable metadata file) must have at least the 2 following column : | |
281 | Id : column to identify masses in the tsv input file | |
282 | Masses : column with all the masses in the tsv input file | |
283 | RT : (optional) column with all the retention time in the tsv input file | |
284 | | |
285 | |
286 personal data bank file must contain certain columns : | |
287 | Masses (Mandatory) and RT (optional) | |
288 | | |
289 | |
290 ---------- | |
291 Parameters | |
292 ---------- | |
293 | |
294 Would you use a file | |
295 | Choose whether the masses are in a file or entered manually | |
296 | YES (default) : parameters **File of masses ; Do you have a header ; Column of Id ; Column of masses** are visible | |
297 | NO : parameter **Mass to submit** is visible | |
298 | | |
299 | |
300 | |
301 If 'use file'='YES' | |
302 | |
303 File of masses | |
304 | see "Input files" section above | |
305 | Tabular file format, Generally variable metadata file | |
306 | | |
307 | |
308 Do you have a header | |
309 | YES (default) : parameter **Number of header lines** is visible | |
310 | NO : all lines are considered to contain masses | |
311 | | |
312 | |
313 If 'have a header'='YES' | |
314 | |
315 Number of header lines | |
316 | Number of lines not containing masses values, these lines will be ignored | |
317 | | |
318 | |
319 In all header cases : | |
320 | |
321 Column of Id | |
322 | Specify the column number for the id in the tsv input file | |
323 | | |
324 | |
325 Would you use retention time (RT) | |
326 | YES (default) : parameter **Column of retention time (RT)** and **Delta of retention time (RT) (in minutes)** are visible | |
327 | NO : Search will be made solely on the basis of the masses | |
328 | | |
329 | |
330 If 'Would you use retention time (RT)'='YES' | |
331 | |
332 Column of retention time (RT) | |
333 | Specify the column number for the retention time (RT) in the tsv input file | |
334 | | |
335 | |
336 Delta of retention time (RT) (in minutes) | |
337 | Specify a delta to apply on retention time - This value is a float. | |
338 | | |
339 | |
340 In all RT cases : | |
341 | |
342 Column of masses | |
343 | Specify the column number for the mass in the tsv input file | |
344 | | |
345 | |
346 | |
347 If 'use file'='NO' | |
348 | |
349 Would you use retention time (RT) | |
350 | YES (default) : parameter **retention time (RT) to submit** and **Delta of retention time (RT) (in minutes)** are visible | |
351 | NO : Search will be made solely on the basis of the masses | |
352 | | |
353 | |
354 If 'Would you use retention time (RT)'='YES' | |
355 | |
356 retention time (RT) to submit | |
357 | Specify a list of retention time to request | |
358 | one or more retention time entered manually | |
359 | For a RT list, writes : rt1 rt2 rt3 | |
360 | You must separate yours values with space | |
361 | dot (.) is for float number | |
362 | | |
363 Delta of retention time (RT) (in minutes) | |
364 | Specify a delta to apply on retention time - This value is a float. | |
365 | | |
366 | |
367 In all RT cases : | |
368 | |
369 Mass to submit | |
370 | Specify a list of mass to request | |
371 | one or more mass(es) entered manually | |
372 | For a masses list, writes : m1 m2 m3 | |
373 | You must separate yours values with space | |
374 | dot (.) is for float number | |
375 | | |
376 | |
377 In all cases : | |
378 | |
379 Delta type | |
380 | Specify a delta type : "in Dalton" or "in ppm" | |
381 | | |
382 | |
383 Delta of mass ("in Dalton" or "in ppm" according to choice) | |
384 | Specify a delta to apply on mass - This value is a float. | |
385 | | |
386 | |
387 Use personal data bank | |
388 | YES : parameter **Bank file**, **Column of masses (MZ) in Bank file** and **Column of retention time (RT) in Bank file** (optional) are visible, the search will be made only on the information of the file | |
389 | NO : a internal bank will be used | |
390 | | |
391 | |
392 If 'Use personal data bank'='YES' | |
393 | |
394 Bank file | |
395 | see "Input files" section above | |
396 | Tabular file format, Generally variable metadata file | |
397 | | |
398 | |
399 Column of masses | |
400 | Specify the column number for the mass in the bank input file | |
401 | | |
402 | |
403 Have you used the retention time (RT) for your input data | |
404 | Answering same as for "Would you use retention time (RT)" | |
405 | YES (default) : parameter **Column of retention time (RT) in Bank file** is visible | |
406 | NO : Search will be made solely on the basis of the masses | |
407 | | |
408 | |
409 Column of retention time (RT) in Bank file | |
410 | Specify the column number for the rt in the bank input file | |
411 | | |
412 | |
413 | |
414 ------------ | |
415 Output files | |
416 ------------ | |
417 | |
418 Two types of files (if you manually enter the masses both files are mingled): | |
419 | bank_inhouse_(input.name)_TSV.tabular : for linking with others modules. | |
420 | | |
421 | bank_inhouse_(input.name)_XLS.tabular : an excel-like output will be available. | |
422 | | |
423 | |
424 | |
425 --------------------------------------------------- | |
426 | |
427 | |
428 --------------- | |
429 Working example | |
430 --------------- | |
431 | |
432 | |
433 .. class:: warningmark | |
434 | |
435 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto | |
436 | Format Data For Postprocessing | |
437 | Perform LCMS Annotations | |
438 | |
439 .. class:: warningmark | |
440 | |
441 And their "W4M courses 2016": | |
442 | Using Galaxy4Metabolomics - W4M table format for Galaxy | |
443 | Annotation Banks - Annotation | |
444 | |
445 ]]></help> | |
446 </tool> |