Mercurial > repos > lecorguille > xcms_xcmsset
comparison abims_xcms_xcmsSet.xml @ 5:588b0a7ae4b0 draft
planemo upload
author | lecorguille |
---|---|
date | Mon, 22 Feb 2016 16:25:05 -0500 |
parents | c5fa73f1703f |
children | 0888f7ef739a |
comparison
equal
deleted
inserted
replaced
4:c5fa73f1703f | 5:588b0a7ae4b0 |
---|---|
1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2"> | 1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7"> |
2 | 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> | 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> |
4 | 4 |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="3.1.2">R</requirement> | 6 <requirement type="package" version="3.1.2">R</requirement> |
7 <requirement type="binary">Rscript</requirement> | 7 <requirement type="binary">Rscript</requirement> |
8 <requirement type="package" version="1.44.0">xcms</requirement> | 8 <requirement type="package" version="1.44.0">xcms</requirement> |
9 <requirement type="package" version="2.1">xcms_w4m_script</requirement> | 9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> |
10 </requirements> | 10 </requirements> |
11 | 11 |
12 <stdio> | 12 <stdio> |
13 <exit_code range="1:" level="fatal" /> | 13 <exit_code range="1:" level="fatal" /> |
14 </stdio> | 14 </stdio> |
15 | 15 |
16 <command> | 16 <command><![CDATA[ |
17 xcms.r | 17 xcms.r |
18 #if $inputs.input == "lib": | 18 #if $inputs.input == "lib": |
19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library | 19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library |
20 #elif $inputs.input == "zip_file": | 20 #elif $inputs.input == "zip_file": |
21 zipfile $inputs.zip_file | 21 zipfile $inputs.zip_file |
22 #end if | 22 #end if |
23 | 23 |
24 xfunction xcmsSet | 24 xfunction xcmsSet |
25 | |
26 xsetRdataOutput $xsetRData | |
27 sampleMetadataOutput $sampleMetadata | |
28 ticspdf $ticsRawPdf | |
29 bicspdf $bpcsRawPdf | |
30 | |
25 ## profmethod $profmethod | 31 ## profmethod $profmethod |
26 nSlaves \${GALAXY_SLOTS:-1} method $methods.method | 32 nSlaves \${GALAXY_SLOTS:-1} method $methods.method |
27 #if $methods.method == "centWave": | 33 #if $methods.method == "centWave": |
28 ppm $methods.ppm | 34 ppm $methods.ppm |
29 peakwidth "c($methods.peakwidth)" | 35 peakwidth "c($methods.peakwidth)" |
30 #if $methods.options_scanrange.option == "show": | 36 #if $methods.options_scanrange.option == "show": |
31 scanrange "c($methods.options_scanrange.scanrange)" | 37 scanrange "c($methods.options_scanrange.scanrange)" |
32 #end if | 38 #end if |
33 #if $methods.options_c.option == "show": | 39 #if $methods.options_c.option == "show": |
34 mzdiff $methods.options_c.mzdiff | 40 mzdiff $methods.options_c.mzdiff |
35 snthresh $methods.options_c.snthresh | 41 snthresh $methods.options_c.snthresh |
36 integrate $methods.options_c.integrate | 42 integrate $methods.options_c.integrate |
37 noise $methods.options_c.noise | 43 noise $methods.options_c.noise |
38 prefilter "c($methods.options_c.prefilter)" | 44 prefilter "c($methods.options_c.prefilter)" |
39 #end if | 45 #end if |
40 #elif $methods.method == "matchedFilter": | 46 #elif $methods.method == "matchedFilter": |
41 step $methods.step | 47 step $methods.step |
42 fwhm $methods.fwhm | 48 fwhm $methods.fwhm |
43 #if $methods.options_m.option == "show": | 49 #if $methods.options_m.option == "show": |
44 ## sigma "$methods.options_m.sigma" | 50 ## sigma "$methods.options_m.sigma" |
54 winSize.noise $methods.winSize_noise | 60 winSize.noise $methods.winSize_noise |
55 amp.Th $methods.amp_Th | 61 amp.Th $methods.amp_Th |
56 scales "c($methods.scales)" | 62 scales "c($methods.scales)" |
57 SNR.method "$methods.SNR_method" | 63 SNR.method "$methods.SNR_method" |
58 #end if | 64 #end if |
59 && (mv xcmsSet.RData $xsetRData; | 65 ; |
60 mv sampleMetadata.tsv $sampleMetadata; | 66 return=\$?; |
61 mv TICs_raw.pdf $ticsRawPdf; | 67 mv log.txt $log; |
62 mv BPCs_raw.pdf $bpcsRawPdf; | 68 cat $log; |
63 mv xset.log $log); | 69 sh -c "exit \$return" |
64 cat $log | 70 ]]></command> |
65 </command> | |
66 | 71 |
67 <inputs> | 72 <inputs> |
68 | 73 |
69 <conditional name="inputs"> | 74 <conditional name="inputs"> |
70 <param name="input" type="select" label="Choose your inputs method" > | 75 <param name="input" type="select" label="Choose your inputs method" > |
71 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> | 76 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> |
72 <option value="lib" >Library directory name</option> | 77 <option value="lib" >Library directory name</option> |
73 </param> | 78 </param> |
74 <when value="zip_file"> | 79 <when value="zip_file"> |
75 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" /> | 80 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> |
76 </when> | 81 </when> |
77 <when value="lib"> | 82 <when value="lib"> |
78 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > | 83 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > |
79 <validator type="empty_field"/> | 84 <validator type="empty_field"/> |
80 </param> | 85 </param> |
110 </param> | 115 </param> |
111 <when value="show"> | 116 <when value="show"> |
112 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" > | 117 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" > |
113 <validator type="empty_field"/> | 118 <validator type="empty_field"/> |
114 </param> | 119 </param> |
120 </when> | |
121 <when value="hide"> | |
115 </when> | 122 </when> |
116 </conditional> | 123 </conditional> |
117 | 124 |
118 <conditional name="options_c"> | 125 <conditional name="options_c"> |
119 <param name="option" type="select" label="Advanced options" > | 126 <param name="option" type="select" label="Advanced options" > |
127 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> | 134 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> |
128 <option value="2">peak limits based on real data (more sensitive to noise)</option> | 135 <option value="2">peak limits based on real data (more sensitive to noise)</option> |
129 </param> | 136 </param> |
130 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> | 137 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/> |
131 <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> | 138 <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/> |
139 </when> | |
140 <when value="hide"> | |
132 </when> | 141 </when> |
133 </conditional> | 142 </conditional> |
134 </when> | 143 </when> |
135 | 144 |
136 <!-- matched Filter options --> | 145 <!-- matched Filter options --> |
151 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> | 160 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> |
152 <!-- | 161 <!-- |
153 <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " /> | 162 <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " /> |
154 --> | 163 --> |
155 </when> | 164 </when> |
165 <when value="hide"> | |
166 </when> | |
156 </conditional> | 167 </conditional> |
157 </when> | 168 </when> |
158 | 169 |
159 <!-- MSW Filter options --> | 170 <!-- MSW Filter options --> |
160 <when value="MSW"> | 171 <when value="MSW"> |
188 <param name="methods.fwhm" value="4" /> | 199 <param name="methods.fwhm" value="4" /> |
189 <param name="methods.options_m.option" value="show" /> | 200 <param name="methods.options_m.option" value="show" /> |
190 <param name="methods.options_m.max" value="50" /> | 201 <param name="methods.options_m.max" value="50" /> |
191 <param name="methods.options_m.snthresh" value="1" /> | 202 <param name="methods.options_m.snthresh" value="1" /> |
192 <param name="methods.options_m.steps" value="2" /> | 203 <param name="methods.options_m.steps" value="2" /> |
193 <output name="xsetRData" file="xset.RData" /> | 204 <!--<output name="xsetRData" file="xset.RData" />--> |
194 <output name="sampleMetadata" file="sampleMetadata.tsv" /> | 205 <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />--> |
195 <output name="ticsRawPdf" file="xset.TICs_raw.pdf" /> | 206 <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />--> |
196 <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" /> | 207 <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />--> |
197 <output name="log" file="xset.log.txt" /> | 208 <output name="log"> |
209 <assert_contents> | |
210 <has_text text="object with 9 samples" /> | |
211 <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" /> | |
212 <has_text text="Mass range: 50.0019-999.9863 m/z" /> | |
213 <has_text text="Peaks: 135846 (about 15094 per sample)" /> | |
214 <has_text text="Peak Groups: 0" /> | |
215 <has_text text="Sample classes: bio, blank" /> | |
216 </assert_contents> | |
217 </output> | |
198 </test> | 218 </test> |
199 </tests> | 219 </tests> |
200 | 220 |
201 <help> | 221 <help><![CDATA[ |
202 | 222 |
203 .. class:: infomark | 223 .. class:: infomark |
204 | 224 |
205 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu | 225 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu |
206 | 226 |
282 You have two methods for your inputs: | 302 You have two methods for your inputs: |
283 | 303 |
284 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). | 304 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories). |
285 | 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. | 305 | 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. |
286 | 306 |
307 Steps for creating the zip file | |
308 ------------------------------- | |
309 | |
310 **Step1: Creating your directory and hierarchize the subdirectories** | |
311 | |
312 | |
313 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). | |
314 | |
315 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild): | |
316 arabidopsis/wild/01.raw | |
317 arabidopsis/mutant/01.raw | |
318 | |
319 **Step2: Creating a zip file** | |
320 | |
321 Create your zip file (e.g.: arabidopsis.zip). | |
322 | |
323 **Step 3 : Uploading it to our Galaxy server** | |
324 | |
325 If your zip file is less than 2Gb, you get use the Get Data tool to upload it. | |
326 | |
327 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf). | |
328 | |
329 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org). | |
330 | |
331 Advices for converting your files for the XCMS input | |
332 ---------------------------------------------------- | |
333 | |
334 We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method. | |
335 | |
336 **We recommend you the following parameters:** | |
337 | |
338 Use Filtering: **True** | |
339 | |
340 Use Peak Picking: **True** | |
341 | |
342 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode | |
343 | |
344 Use zlib: **64** | |
345 | |
346 Binary Encoding: **64** | |
347 | |
348 m/z Encoding: **64** | |
349 | |
350 Intensity Encoding: **64** | |
351 | |
352 | |
287 ---------- | 353 ---------- |
288 Parameters | 354 Parameters |
289 ---------- | 355 ---------- |
290 | 356 |
291 Extraction method for peaks detection | 357 Extraction method for peaks detection |
390 | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :** | 456 | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :** |
391 | 457 |
392 .. image:: xcms_tics.png | 458 .. image:: xcms_tics.png |
393 | 459 |
394 | 460 |
395 | 461 --------------------------------------------------- |
396 </help> | 462 |
463 Changelog/News | |
464 -------------- | |
465 | |
466 | |
467 **Version 2.0.7 - 10/02/2016** | |
468 | |
469 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
470 | |
471 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters | |
472 | |
473 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer | |
474 | |
475 - UPDATE: refactoring of internal management of inputs/outputs | |
476 | |
477 - UPDATE: refactoring to feed the new report tool | |
478 | |
479 | |
480 **Version 2.0.2 - 18/01/2016 | |
481 | |
482 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. | |
483 | |
484 | |
485 **Version 2.0.2 - 09/10/2015** | |
486 | |
487 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows. | |
488 | |
489 | |
490 **Version 2.0.2 - 02/06/2015** | |
491 | |
492 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible. | |
493 | |
494 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
495 | |
496 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
497 | |
498 ]]></help> | |
397 | 499 |
398 | 500 |
399 <citations> | 501 <citations> |
400 <citation type="doi">10.1021/ac051437y</citation> | 502 <citation type="doi">10.1021/ac051437y</citation> |
401 <citation type="doi">10.1093/bioinformatics/btu813</citation> | 503 <citation type="doi">10.1093/bioinformatics/btu813</citation> |