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comparison abims_xcms_xcmsSet.xml @ 11:91311aa08cdc draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author lecorguille
date Mon, 30 Jan 2017 08:52:59 -0500
parents 69eb0fc05837
children 15646e937936
comparison
equal deleted inserted replaced
10:69eb0fc05837 11:91311aa08cdc
1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.9"> 1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.11">
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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 @COMMAND_XCMS_SCRIPT@ 13 @COMMAND_XCMS_SCRIPT@
14 #if $inputs.input == "lib": 14 #if $inputs.input == "lib":
15 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library 15 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
16 #elif $inputs.input == "zip_file": 16 #elif $inputs.input == "zip_file":
22 xsetRdataOutput $xsetRData 22 xsetRdataOutput $xsetRData
23 sampleMetadataOutput $sampleMetadata 23 sampleMetadataOutput $sampleMetadata
24 ticspdf $ticsRawPdf 24 ticspdf $ticsRawPdf
25 bicspdf $bpcsRawPdf 25 bicspdf $bpcsRawPdf
26 26
27 ## profmethod $profmethod 27
28 nSlaves \${GALAXY_SLOTS:-1} method $methods.method 28 #if $options_scanrange.option == "show":
29 scanrange "c($options_scanrange.scanrange)"
30 #end if
31
32 ## profmethod $profmethod
33 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
29 #if $methods.method == "centWave": 34 #if $methods.method == "centWave":
30 ppm $methods.ppm 35 ppm $methods.ppm
31 peakwidth "c($methods.peakwidth)" 36 peakwidth "c($methods.peakwidth)"
32 #if $methods.options_scanrange.option == "show":
33 scanrange "c($methods.options_scanrange.scanrange)"
34 #end if
35 #if $methods.options_c.option == "show": 37 #if $methods.options_c.option == "show":
36 mzdiff $methods.options_c.mzdiff 38 mzdiff $methods.options_c.mzdiff
37 snthresh $methods.options_c.snthresh 39 snthresh $methods.options_c.snthresh
38 integrate $methods.options_c.integrate 40 integrate $methods.options_c.integrate
39 noise $methods.options_c.noise 41 noise $methods.options_c.noise
58 scales "c($methods.scales)" 60 scales "c($methods.scales)"
59 SNR.method "$methods.SNR_method" 61 SNR.method "$methods.SNR_method"
60 #end if 62 #end if
61 @COMMAND_LOG_EXIT@ 63 @COMMAND_LOG_EXIT@
62 ]]></command> 64 ]]></command>
63 65
64 <inputs> 66 <inputs>
65 67
66 <conditional name="inputs"> 68 <conditional name="inputs">
67 <param name="input" type="select" label="Choose your inputs method" > 69 <param name="input" type="select" label="Choose your inputs method" >
68 <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 <when value="zip_file"> 73 <when value="zip_file">
72 <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" />
73 </when> 75 </when>
74 <when value="lib"> 76 <when value="lib">
75 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" > 77 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
76 <validator type="empty_field"/> 78 <validator type="empty_field"/>
77 </param> 79 </param>
78 </when> 80 </when>
79 81
80 </conditional> 82 </conditional>
81 83
82 84 <conditional name="options_scanrange">
85 <param name="option" type="select" label="Scan range option " >
86 <option value="show">show</option>
87 <option value="hide" selected="true">hide</option>
88 </param>
89 <when value="show">
90 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
91 <validator type="empty_field"/>
92 </param>
93 </when>
94 <when value="hide">
95 </when>
96 </conditional>
97
98
83 <!-- 99 <!--
84 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" > 100 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
85 <option value="bin" selected="true">bin</option> 101 <option value="bin" selected="true">bin</option>
86 <option value="binlin">binlin</option> 102 <option value="binlin">binlin</option>
87 <option value="binlinbase">binlinbase</option> 103 <option value="binlinbase">binlinbase</option>
98 114
99 <!-- centWave Filter options --> 115 <!-- centWave Filter options -->
100 <when value="centWave"> 116 <when value="centWave">
101 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" /> 117 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
102 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" /> 118 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
103 <conditional name="options_scanrange"> 119
104 <param name="option" type="select" label="Scan range option " >
105 <option value="show">show</option>
106 <option value="hide" selected="true">hide</option>
107 </param>
108 <when value="show">
109 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
110 <validator type="empty_field"/>
111 </param>
112 </when>
113 <when value="hide">
114 </when>
115 </conditional>
116
117 <conditional name="options_c"> 120 <conditional name="options_c">
118 <param name="option" type="select" label="Advanced options" > 121 <param name="option" type="select" label="Advanced options" >
119 <option value="show">show</option> 122 <option value="show">show</option>
120 <option value="hide" selected="true">hide</option> 123 <option value="hide" selected="true">hide</option>
121 </param> 124 </param>
132 <when value="hide"> 135 <when value="hide">
133 </when> 136 </when>
134 </conditional> 137 </conditional>
135 </when> 138 </when>
136 139
137 <!-- matched Filter options --> 140 <!-- matched Filter options -->
138 <when value="matchedFilter"> 141 <when value="matchedFilter">
139 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> 142 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
140 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> 143 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
141 <conditional name="options_m"> 144 <conditional name="options_m">
142 <param name="option" type="select" label="Advanced options" > 145 <param name="option" type="select" label="Advanced options" >
157 <when value="hide"> 160 <when value="hide">
158 </when> 161 </when>
159 </conditional> 162 </conditional>
160 </when> 163 </when>
161 164
162 <!-- MSW Filter options --> 165 <!-- MSW Filter options -->
163 <when value="MSW"> 166 <when value="MSW">
164 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" > 167 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
165 <option value="TRUE">TRUE</option> 168 <option value="TRUE">TRUE</option>
166 <option value="FALSE">FALSE</option> 169 <option value="FALSE">FALSE</option>
167 </param> 170 </param>
171 <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " /> 174 <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
172 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." /> 175 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
173 </when> 176 </when>
174 </conditional> 177 </conditional>
175 </inputs> 178 </inputs>
176 179
177 <outputs> 180 <outputs>
178 <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" /> 181 <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
179 <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" /> 182 <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
180 <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" /> 183 <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" />
181 <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" /> 184 <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" />
182 <data name="log" format="txt" label="xset.log.txt" /> 185 <data name="log" format="txt" label="xset.log.txt" />
183 </outputs> 186 </outputs>
184 187
185 <tests> 188 <tests>
186 <!--<test> 189 <!--<test>
187 <param name="inputs|input" value="zip_file" /> 190 <param name="inputs|input" value="zip_file" />
188 <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> 191 <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
189 <param name="methods|method" value="matchedFilter" /> 192 <param name="methods|method" value="matchedFilter" />
237 <has_text text="Sample classes: KO, WT" /> 240 <has_text text="Sample classes: KO, WT" />
238 </assert_contents> 241 </assert_contents>
239 </output> 242 </output>
240 </test> 243 </test>
241 </tests> 244 </tests>
242 245
243 <help><![CDATA[ 246 <help><![CDATA[
244 247
245 @HELP_AUTHORS@ 248 @HELP_AUTHORS@
246 249
247 ============ 250 ============
265 **Upstream tools** 268 **Upstream tools**
266 269
267 ========================= ================= ======= ========= 270 ========================= ================= ======= =========
268 Name output file format parameter 271 Name output file format parameter
269 ========================= ================= ======= ========= 272 ========================= ================= ======= =========
270 NA NA zip NA 273 NA NA zip NA
271 ========================= ================= ======= ========= 274 ========================= ================= ======= =========
272 275
273 276
274 **Downstream tools** 277 **Downstream tools**
275 278
289 .. image:: XCMS_Galaxy_workflow.png 292 .. image:: XCMS_Galaxy_workflow.png
290 293
291 294
292 ------ 295 ------
293 296
294 .. class:: infomark 297 .. class:: infomark
295 298
296 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. 299 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
297 300
298 --------------------------------------------------- 301 ---------------------------------------------------
299 302
369 Extraction method for peaks detection 372 Extraction method for peaks detection
370 ------------------------------------- 373 -------------------------------------
371 374
372 **Matched Filter** 375 **Matched Filter**
373 376
374 | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm. 377 | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
375 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002). 378 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
376 379
377 380
378 **cent Wave** 381 **cent Wave**
379 382
407 | This file is necessary in the Anova and PCA step of the workflow. 410 | This file is necessary in the Anova and PCA step of the workflow.
408 411
409 xset.RData: rdata.xcms.raw format 412 xset.RData: rdata.xcms.raw format
410 413
411 | Rdata file that is necessary in the second step of the workflow "xcms.group". 414 | Rdata file that is necessary in the second step of the workflow "xcms.group".
412 415
413 ------ 416 ------
414 417
415 .. class:: infomark 418 .. class:: infomark
416 419
417 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool. 420 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
418 421
419 --------------------------------------------------- 422 ---------------------------------------------------
420 423
430 Parameters 433 Parameters
431 ---------- 434 ----------
432 435
433 | Method -> **matchedFilter** 436 | Method -> **matchedFilter**
434 | step -> **0.01** 437 | step -> **0.01**
435 | fwhm -> **4** 438 | fwhm -> **4**
436 | Advanced option -> **show** 439 | Advanced option -> **show**
437 | max: -> **50** 440 | max: -> **50**
438 | snthresh -> **1** 441 | snthresh -> **1**
439 | steps -> **2** 442 | steps -> **2**
440 443
473 --------------------------------------------------- 476 ---------------------------------------------------
474 477
475 Changelog/News 478 Changelog/News
476 -------------- 479 --------------
477 480
481 **Version 2.0.11 - 22/12/2016**
482
483 - BUGFIX: propose scanrange for all methods
484
485 **Version 2.0.10 - 22/12/2016**
486
487 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
488
478 **Version 2.0.9 - 06/07/2016** 489 **Version 2.0.9 - 06/07/2016**
479 490
480 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 491 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
481 492
482 **Version 2.0.8 - 06/04/2016** 493 **Version 2.0.8 - 06/04/2016**
483 494
484 - TEST: refactoring to pass planemo test using conda dependencies 495 - TEST: refactoring to pass planemo test using conda dependencies
485 496