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comparison abims_xcms_xcmsSet.xml @ 5:588b0a7ae4b0 draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:25:05 -0500
parents c5fa73f1703f
children 0888f7ef739a
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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 &amp;&amp; (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>