Mercurial > repos > lecorguille > xcms_xcmsset

comparison abims_xcms_xcmsSet.xml @ 17:602acc32b549 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
author lecorguille
date Sun, 05 Feb 2017 08:55:49 -0500
parents f28041d2180a
children d7971ea3ad1d
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16:f28041d2180a 17:602acc32b549
1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.11"> 1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
2
3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description> 2 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
4 3
5 <macros> 4 <macros>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 </macros> 6 </macros>
9 <expand macro="requirements"/> 8 <expand macro="requirements"/>
10 <expand macro="stdio"/> 9 <expand macro="stdio"/>
11 10
12 <command><![CDATA[ 11 <command><![CDATA[
13 @COMMAND_XCMS_SCRIPT@ 12 @COMMAND_XCMS_SCRIPT@
14 #if $inputs.input == "lib": 13
15 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library 14 #if $inputs.input == "zip_file":
16 #elif $inputs.input == "zip_file":
17 zipfile $inputs.zip_file 15 zipfile $inputs.zip_file
16 #elif $inputs.input == "single_file":
17 singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
18 #end if 18 #end if
19 19
20 xfunction xcmsSet 20 xfunction xcmsSet
21 21
22 xsetRdataOutput $xsetRData 22 xsetRdataOutput $xsetRData
63 @COMMAND_LOG_EXIT@ 63 @COMMAND_LOG_EXIT@
64 ]]></command> 64 ]]></command>
65 65
66 <inputs> 66 <inputs>
67 67
68 <conditional name="inputs"> 68 <conditional name="inputs">
69 <param name="input" type="select" label="Choose your inputs method" > 69 <param name="input" type="select" label="Choose your inputs method" >
70 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> 70 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
71 <option value="lib" >Library directory name</option> 71 <option value="single_file">mzXML file from your history</option>
72 </param> 72 </param>
73 <when value="zip_file"> 73 <when value="zip_file">
74 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> 74 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
75 </when> 75 </when>
76 <when value="lib"> 76 <when value="single_file">
77 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > 77 <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" />
78 <validator type="empty_field"/> 78 </when>
79 </param>
80 </when>
81
82 </conditional> 79 </conditional>
83 80
84 <conditional name="options_scanrange"> 81 <conditional name="options_scanrange">
85 <param name="option" type="select" label="Scan range option " > 82 <param name="option" type="select" label="Scan range option " >
86 <option value="show">show</option> 83 <option value="show">show</option>
101 <option value="bin" selected="true">bin</option> 98 <option value="bin" selected="true">bin</option>
102 <option value="binlin">binlin</option> 99 <option value="binlin">binlin</option>
103 <option value="binlinbase">binlinbase</option> 100 <option value="binlinbase">binlinbase</option>
104 <option value="intlin">intlin</option> 101 <option value="intlin">intlin</option>
105 </param> 102 </param>
106 <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" />
107 --> 103 -->
108 <conditional name="methods"> 104 <conditional name="methods">
109 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below"> 105 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
110 <option value="centWave" >centWave</option> 106 <option value="centWave" >centWave</option>
111 <option value="matchedFilter" selected="true">matchedFilter</option> 107 <option value="matchedFilter" selected="true">matchedFilter</option>
114 110
115 <!-- centWave Filter options --> 111 <!-- centWave Filter options -->
116 <when value="centWave"> 112 <when value="centWave">
117 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> 113 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
118 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" /> 114 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
119 115
120 <conditional name="options_c"> 116 <conditional name="options_c">
121 <param name="option" type="select" label="Advanced options" > 117 <param name="option" type="select" label="Advanced options" >
122 <option value="show">show</option> 118 <option value="show">show</option>
123 <option value="hide" selected="true">hide</option> 119 <option value="hide" selected="true">hide</option>
124 </param> 120 </param>
239 <has_text text="Peak Groups: 0" /> 235 <has_text text="Peak Groups: 0" />
240 <has_text text="Sample classes: KO, WT" /> 236 <has_text text="Sample classes: KO, WT" />
241 </assert_contents> 237 </assert_contents>
242 </output> 238 </output>
243 </test> 239 </test>
240 <!-- Passed by disable to save time for Travis"
241 <!--<test>
242 <param name="inputs|input" value="single_file" />
243 <param name="inputs|single_file" value="ko15.CDF" ftype="netcdf" />
244 <param name="methods|method" value="centWave" />
245 <param name="methods|ppm" value="25" />
246 <param name="methods|peakwidth" value="20,50" />
247 <output name="log">
248 <assert_contents>
249 <has_text text="object with 1 samples" />
250 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
251 <has_text text="Mass range: 200.2-600 m/z" />
252 <has_text text="Peaks: 2262 (about 2262 per sample)" />
253 <has_text text="Peak Groups: 0" />
254 <has_text text="Sample classes: ." />
255 </assert_contents>
256 </output>
257 </test>
258 <test>
259 <param name="inputs|input" value="single_file" />
260 <param name="inputs|single_file" value="ko16.CDF" ftype="netcdf" />
261 <param name="methods|method" value="centWave" />
262 <param name="methods|ppm" value="25" />
263 <param name="methods|peakwidth" value="20,50" />
264 <output name="log">
265 <assert_contents>
266 <has_text text="object with 1 samples" />
267 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
268 <has_text text="Mass range: 200.1-600 m/z" />
269 <has_text text="Peaks: 2408 (about 2408 per sample)" />
270 <has_text text="Peak Groups: 0" />
271 <has_text text="Sample classes: ." />
272 </assert_contents>
273 </output>
274 </test>
275 <test>
276 <param name="inputs|input" value="single_file" />
277 <param name="inputs|single_file" value="wt15.CDF" ftype="netcdf" />
278 <param name="methods|method" value="centWave" />
279 <param name="methods|ppm" value="25" />
280 <param name="methods|peakwidth" value="20,50" />
281 <output name="log">
282 <assert_contents>
283 <has_text text="object with 1 samples" />
284 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
285 <has_text text="Mass range: 200.2-599.8 m/z" />
286 <has_text text="Peaks: 2278 (about 2278 per sample)" />
287 <has_text text="Peak Groups: 0" />
288 <has_text text="Sample classes: ." />
289 </assert_contents>
290 </output>
291 </test>
292 <test>
293 <param name="inputs|input" value="single_file" />
294 <param name="inputs|single_file" value="wt16.CDF" ftype="netcdf" />
295 <param name="methods|method" value="centWave" />
296 <param name="methods|ppm" value="25" />
297 <param name="methods|peakwidth" value="20,50" />
298 <output name="log">
299 <assert_contents>
300 <has_text text="object with 1 samples" />
301 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
302 <has_text text="Mass range: 200.3-600 m/z" />
303 <has_text text="Peaks: 2303 (about 2303 per sample)" />
304 <has_text text="Peak Groups: 0" />
305 <has_text text="Sample classes: ." />
306 </assert_contents>
307 </output>
308 </test>-->
309 <test>
310 <param name="inputs|input" value="single_file" />
311 <param name="inputs|single_file" value="HU_neg_017.mzXML" ftype="mzxml" />
312 <param name="methods|method" value="centWave" />
313 <param name="methods|ppm" value="25" />
314 <param name="methods|peakwidth" value="20,50" />
315 <output name="log">
316 <assert_contents>
317 <has_text text="object with 1 samples" />
318 <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />
319 <has_text text="Mass range: 57.9756-556.8128 m/z" />
320 <has_text text="Peaks: 380 (about 380 per sample)" />
321 <has_text text="Peak Groups: 0" />
322 <has_text text="Sample classes: ." />
323 </assert_contents>
324 </output>
325 </test>
326 <test>
327 <param name="inputs|input" value="single_file" />
328 <param name="inputs|single_file" value="MM14.mzML" ftype="mzxml" />
329 <param name="methods|method" value="centWave" />
330 <param name="methods|ppm" value="56" />
331 <param name="methods|peakwidth" value="5.275,13.5" />
332 <output name="log">
333 <assert_contents>
334 <has_text text="object with 1 samples" />
335 <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
336 <has_text text="Mass range: 117.0357-936.7059 m/z" />
337 <has_text text="Peaks: 222 (about 222 per sample)" />
338 <has_text text="Peak Groups: 0" />
339 <has_text text="Sample classes: ." />
340 </assert_contents>
341 </output>
342 </test>
244 </tests> 343 </tests>
245 344
246 <help><![CDATA[ 345 <help><![CDATA[
247 346
248 @HELP_AUTHORS@ 347 @HELP_AUTHORS@
304 403
305 ----------- 404 -----------
306 Input files 405 Input files
307 ----------- 406 -----------
308 407
309 +---------------------------+------------+ 408 +---------------------------+--------------------+
310 | Parameter : num + label | Format | 409 | Parameter : num + label | Format |
311 +===========================+============+ 410 +===========================+====================+
312 | 1 : Choose your inputs | zip | 411 | OR : Zip file | zip |
313 +---------------------------+------------+ 412 +---------------------------+--------------------+
413 | OR : Single file | mzXML, netCDF |
414 +---------------------------+--------------------+
314 415
315 **Choose your inputs** 416 **Choose your inputs**
316 417
317 You have two methods for your inputs: 418 You have two methods for your inputs:
318 419
319 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). 420 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
320 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories. 421 | Single file: You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
321 422
322 Steps for creating the zip file 423 Zip file: Steps for creating the zip file
323 ------------------------------- 424 -----------------------------------------
324 425
325 **Step1: Creating your directory and hierarchize the subdirectories** 426 **Step1: Creating your directory and hierarchize the subdirectories**
326 427
327 428
328 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug). 429 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
476 --------------------------------------------------- 577 ---------------------------------------------------
477 578
478 Changelog/News 579 Changelog/News
479 -------------- 580 --------------
480 581
582 **Version 2.1.0 - 03/02/2017**
583
584 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
585
481 **Version 2.0.11 - 22/12/2016** 586 **Version 2.0.11 - 22/12/2016**
482 587
483 - BUGFIX: propose scanrange for all methods 588 - BUGFIX: propose scanrange for all methods
484 589
485 **Version 2.0.10 - 22/12/2016** 590 **Version 2.0.10 - 22/12/2016**