Mercurial > repos > lecorguille > xcms_xcmsset
comparison abims_xcms_xcmsSet.xml @ 6:0888f7ef739a draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author | lecorguille |
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date | Fri, 08 Apr 2016 10:38:52 -0400 |
parents | 588b0a7ae4b0 |
children | 451ff602a957 |
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5:588b0a7ae4b0 | 6:0888f7ef739a |
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1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7"> | 1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.8"> |
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 <macros> |
6 <requirement type="package" version="3.1.2">R</requirement> | 6 <import>macros.xml</import> |
7 <requirement type="binary">Rscript</requirement> | 7 </macros> |
8 <requirement type="package" version="1.44.0">xcms</requirement> | 8 |
9 <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> | 9 <expand macro="requirements"/> |
10 </requirements> | 10 <expand macro="stdio"/> |
11 | |
12 <stdio> | |
13 <exit_code range="1:" level="fatal" /> | |
14 </stdio> | |
15 | 11 |
16 <command><![CDATA[ | 12 <command><![CDATA[ |
17 xcms.r | 13 @COMMAND_XCMS_SCRIPT@ |
18 #if $inputs.input == "lib": | 14 #if $inputs.input == "lib": |
19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library | 15 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library |
20 #elif $inputs.input == "zip_file": | 16 #elif $inputs.input == "zip_file": |
21 zipfile $inputs.zip_file | 17 zipfile $inputs.zip_file |
22 #end if | 18 #end if |
31 ## profmethod $profmethod | 27 ## profmethod $profmethod |
32 nSlaves \${GALAXY_SLOTS:-1} method $methods.method | 28 nSlaves \${GALAXY_SLOTS:-1} method $methods.method |
33 #if $methods.method == "centWave": | 29 #if $methods.method == "centWave": |
34 ppm $methods.ppm | 30 ppm $methods.ppm |
35 peakwidth "c($methods.peakwidth)" | 31 peakwidth "c($methods.peakwidth)" |
36 #if $methods.options_scanrange.option == "show": | 32 #if $methods.options_scanrange.option == "show": |
37 scanrange "c($methods.options_scanrange.scanrange)" | 33 scanrange "c($methods.options_scanrange.scanrange)" |
38 #end if | 34 #end if |
39 #if $methods.options_c.option == "show": | 35 #if $methods.options_c.option == "show": |
40 mzdiff $methods.options_c.mzdiff | 36 mzdiff $methods.options_c.mzdiff |
41 snthresh $methods.options_c.snthresh | 37 snthresh $methods.options_c.snthresh |
42 integrate $methods.options_c.integrate | 38 integrate $methods.options_c.integrate |
43 noise $methods.options_c.noise | 39 noise $methods.options_c.noise |
44 prefilter "c($methods.options_c.prefilter)" | 40 prefilter "c($methods.options_c.prefilter)" |
45 #end if | 41 #end if |
46 #elif $methods.method == "matchedFilter": | 42 #elif $methods.method == "matchedFilter": |
47 step $methods.step | 43 step $methods.step |
48 fwhm $methods.fwhm | 44 fwhm $methods.fwhm |
49 #if $methods.options_m.option == "show": | 45 #if $methods.options_m.option == "show": |
50 ## sigma "$methods.options_m.sigma" | 46 ## sigma "$methods.options_m.sigma" |
60 winSize.noise $methods.winSize_noise | 56 winSize.noise $methods.winSize_noise |
61 amp.Th $methods.amp_Th | 57 amp.Th $methods.amp_Th |
62 scales "c($methods.scales)" | 58 scales "c($methods.scales)" |
63 SNR.method "$methods.SNR_method" | 59 SNR.method "$methods.SNR_method" |
64 #end if | 60 #end if |
65 ; | 61 @COMMAND_LOG_EXIT@ |
66 return=\$?; | |
67 mv log.txt $log; | |
68 cat $log; | |
69 sh -c "exit \$return" | |
70 ]]></command> | 62 ]]></command> |
71 | 63 |
72 <inputs> | 64 <inputs> |
73 | 65 |
74 <conditional name="inputs"> | 66 <conditional name="inputs"> |
190 <data name="log" format="txt" label="xset.log.txt" /> | 182 <data name="log" format="txt" label="xset.log.txt" /> |
191 </outputs> | 183 </outputs> |
192 | 184 |
193 <tests> | 185 <tests> |
194 <test> | 186 <test> |
195 <param name="inputs.input" value="zip_file" /> | 187 <param name="inputs|input" value="zip_file" /> |
196 <param name="inputs.zip_file" value="sacuri.zip" /> | 188 <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> |
197 <param name="methods.method" value="matchedFilter" /> | 189 <param name="methods|method" value="matchedFilter" /> |
198 <param name="methods.step" value="0.01" /> | 190 <param name="methods|step" value="0.01" /> |
199 <param name="methods.fwhm" value="4" /> | 191 <param name="methods|fwhm" value="4" /> |
200 <param name="methods.options_m.option" value="show" /> | 192 <param name="methods|options_m|option" value="show" /> |
201 <param name="methods.options_m.max" value="50" /> | 193 <param name="methods|options_m|max" value="50" /> |
202 <param name="methods.options_m.snthresh" value="1" /> | 194 <param name="methods|options_m|snthresh" value="1" /> |
203 <param name="methods.options_m.steps" value="2" /> | 195 <param name="methods|options_m|steps" value="2" /> |
204 <!--<output name="xsetRData" file="xset.RData" />--> | |
205 <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />--> | |
206 <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />--> | |
207 <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />--> | |
208 <output name="log"> | 196 <output name="log"> |
209 <assert_contents> | 197 <assert_contents> |
210 <has_text text="object with 9 samples" /> | 198 <has_text text="object with 4 samples" /> |
211 <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" /> | 199 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> |
212 <has_text text="Mass range: 50.0019-999.9863 m/z" /> | 200 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
213 <has_text text="Peaks: 135846 (about 15094 per sample)" /> | 201 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
202 <has_text text="Peak Groups: 0" /> | |
203 <has_text text="Sample classes: bio, blank" /> | |
204 </assert_contents> | |
205 </output> | |
206 </test> | |
207 <test> | |
208 <param name="inputs|input" value="zip_file" /> | |
209 <param name="inputs|zip_file" value="sacuri_current_root.zip" ftype="zip" /> | |
210 <param name="methods|method" value="centWave" /> | |
211 <param name="methods|ppm" value="25" /> | |
212 <param name="methods|peakwidth" value="20,50" /> | |
213 <output name="log"> | |
214 <assert_contents> | |
215 <has_text text="object with 4 samples" /> | |
216 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" /> | |
217 <has_text text="Mass range: 57.9756-593.4086 m/z" /> | |
218 <has_text text="Peaks: 1535 (about 384 per sample)" /> | |
214 <has_text text="Peak Groups: 0" /> | 219 <has_text text="Peak Groups: 0" /> |
215 <has_text text="Sample classes: bio, blank" /> | 220 <has_text text="Sample classes: bio, blank" /> |
216 </assert_contents> | 221 </assert_contents> |
217 </output> | 222 </output> |
218 </test> | 223 </test> |
219 </tests> | 224 </tests> |
220 | 225 |
221 <help><![CDATA[ | 226 <help><![CDATA[ |
222 | 227 |
223 .. class:: infomark | 228 @HELP_AUTHORS@ |
224 | |
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 | |
226 | |
227 .. class:: infomark | |
228 | |
229 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] | |
230 | |
231 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. | |
232 | |
233 --------------------------------------------------- | |
234 | 229 |
235 ============ | 230 ============ |
236 Xcms.xcmsSet | 231 Xcms.xcmsSet |
237 ============ | 232 ============ |
238 | 233 |
461 --------------------------------------------------- | 456 --------------------------------------------------- |
462 | 457 |
463 Changelog/News | 458 Changelog/News |
464 -------------- | 459 -------------- |
465 | 460 |
461 **Version 2.0.8 - 06/04/2016** | |
462 | |
463 - TEST: refactoring to pass planemo test using conda dependencies | |
464 | |
466 | 465 |
467 **Version 2.0.7 - 10/02/2016** | 466 **Version 2.0.7 - 10/02/2016** |
468 | 467 |
469 - BUGFIX: better management of errors. Datasets remained green although the process failed | 468 - BUGFIX: better management of errors. Datasets remained green although the process failed |
470 | 469 |
472 | 471 |
473 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer | 472 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer |
474 | 473 |
475 - UPDATE: refactoring of internal management of inputs/outputs | 474 - UPDATE: refactoring of internal management of inputs/outputs |
476 | 475 |
477 - UPDATE: refactoring to feed the new report tool | 476 - TEST: refactoring to feed the new report tool |
478 | 477 |
479 | 478 |
480 **Version 2.0.2 - 18/01/2016 | 479 **Version 2.0.2 - 18/01/2016 |
481 | 480 |
482 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. | 481 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases. |
495 | 494 |
496 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | 495 - IMPROVEMENT: parameter labels have changed to facilitate their reading. |
497 | 496 |
498 ]]></help> | 497 ]]></help> |
499 | 498 |
500 | 499 <expand macro="citation" /> |
501 <citations> | |
502 <citation type="doi">10.1021/ac051437y</citation> | |
503 <citation type="doi">10.1093/bioinformatics/btu813</citation> | |
504 </citations> | |
505 | |
506 </tool> | 500 </tool> |