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comparison abims_xcms_group.xml @ 10:c81275aee959 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author lecorguille
date Fri, 07 Apr 2017 07:35:31 -0400
parents 5d80e7511dfb
children 9e45e1c404a4
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9:2c1d7df89cf6 10:c81275aee959
1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.6"> 1 <tool id="abims_xcms_group" name="xcms.group" version="2.1.0">
2 2
3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description> 3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
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 xfunction group 14 xfunction group
15 image $image 15 image '$image'
16 16
17 xsetRdataOutput $xsetRData 17 xsetRdataOutput '$xsetRData'
18 rplotspdf $rplotsPdf 18 rplotspdf '$rplotsPdf'
19 19
20 method $methods.method sleep 0.001 20 method $methods.method sleep 0.001
21 #if $methods.method == "density": 21 #if $methods.method == "density":
22 ## minsamp $methods.minsamp 22 ## minsamp $methods.minsamp
23 minfrac $methods.minfrac 23 minfrac $methods.minfrac
24 bw $methods.bw 24 bw $methods.bw
25 mzwid $methods.mzwid 25 mzwid $methods.mzwid
26 #if $methods.density_options.option == "show": 26 #if $methods.density_options.option == "show":
27 max $methods.density_options.max 27 max $methods.density_options.max
28 #end if 28 #end if
29 #elif $methods.method == "mzClust": 29 #elif $methods.method == "mzClust":
30 mzppm $methods.mzppm 30 mzppm $methods.mzppm
31 mzabs $methods.mzabs 31 mzabs $methods.mzabs
32 minfrac $methods.minfrac 32 minfrac $methods.minfrac
33 ## minsamp $methods.minsamp 33 ## minsamp $methods.minsamp
35 mzVsRTbalance $methods.mzVsRTbalance 35 mzVsRTbalance $methods.mzVsRTbalance
36 mzCheck $methods.mzCheck 36 mzCheck $methods.mzCheck
37 rtCheck $methods.rtCheck 37 rtCheck $methods.rtCheck
38 kNN $methods.kNN 38 kNN $methods.kNN
39 #end if 39 #end if
40
41 @COMMAND_PEAKLIST@
42
40 @COMMAND_LOG_EXIT@ 43 @COMMAND_LOG_EXIT@
41 ]]></command> 44 ]]></command>
42 45
43 <inputs> 46 <inputs>
44 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 47 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
45 <conditional name="methods"> 48 <conditional name="methods">
46 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> 49 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
51 <when value="density"> 54 <when value="density">
52 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" /> 55 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
53 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" /> 56 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
54 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " /> 57 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
55 <!-- 58 <!--
56 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> 59 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
57 --> 60 -->
58 <conditional name="density_options"> 61 <conditional name="density_options">
59 <param name="option" type="select" label="Advanced options"> 62 <param name="option" type="select" label="Advanced options">
60 <option value="show">show</option> 63 <option value="show">show</option>
61 <option value="hide" selected="true">hide</option> 64 <option value="hide" selected="true">hide</option>
62 </param> 65 </param>
63 <when value="show"> 66 <when value="show">
64 <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" /> 67 <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
65 </when> 68 </when>
66 <when value="hide"> 69 <when value="hide">
67 </when> 70 </when>
68 </conditional> 71 </conditional>
69 72
71 <when value="mzClust"> 74 <when value="mzClust">
72 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" /> 75 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" />
73 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" /> 76 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" />
74 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" /> 77 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" />
75 <!-- 78 <!--
76 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> 79 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " />
77 --> 80 -->
78 </when> 81 </when>
79 <when value="nearest"> 82 <when value="nearest">
80 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" /> 83 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" />
81 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" /> 84 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" />
82 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" /> 85 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" />
83 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" /> 86 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" />
84 </when> 87 </when>
85 </conditional> 88 </conditional>
86 <!-- 89 <!--
87 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines"> 90 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines">
88 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/> 91 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/>
89 </param> 92 </param>
90 --> 93 -->
91 94
95 <expand macro="input_peaklist"/>
92 </inputs> 96 </inputs>
93 97
94 <outputs> 98 <outputs>
95 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> 99 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
96 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> 100 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
101 <expand macro="output_peaklist" function="group"/>
97 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> 102 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
98 </outputs> 103 </outputs>
99 104
100 <tests> 105 <tests>
101 <!--<test> 106 <!--<test>
123 <param name="methods|bw" value="5"/> 128 <param name="methods|bw" value="5"/>
124 <param name="methods|minfrac" value="0.3"/> 129 <param name="methods|minfrac" value="0.3"/>
125 <param name="methods|mzwid" value="0.01"/> 130 <param name="methods|mzwid" value="0.01"/>
126 <param name="methods|density_options|option" value="show"/> 131 <param name="methods|density_options|option" value="show"/>
127 <param name="methods|density_options|max" value="50"/> 132 <param name="methods|density_options|max" value="50"/>
133 <conditional name="peaklist">
134 <param name="convertRTMinute" value="false" />
135 <param name="peaklistBool" value="true" />
136 <param name="numDigitsMZ" value="4" />
137 <param name="numDigitsRT" value="1" />
138 </conditional>
128 <output name="log"> 139 <output name="log">
129 <assert_contents> 140 <assert_contents>
130 <has_text text="object with 4 samples" /> 141 <has_text text="object with 4 samples" />
131 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> 142 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
132 <has_text text="Mass range: 200.1-600 m/z" /> 143 <has_text text="Mass range: 200.1-600 m/z" />
133 <has_text text="Peaks: 9251 (about 2313 per sample)" /> 144 <has_text text="Peaks: 9251 (about 2313 per sample)" />
134 <has_text text="Peak Groups: 8275" /> 145 <has_text text="Peak Groups: 8275" />
135 <has_text text="Sample classes: KO, WT" /> 146 <has_text text="Sample classes: KO, WT" />
136 </assert_contents> 147 </assert_contents>
137 </output> 148 </output>
149 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
150 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
151 </test>
152 <test>
153 <param name="image" value="faahKO-single-class.xset.merged.RData"/>
154 <param name="methods|method" value="density"/>
155 <param name="methods|bw" value="5"/>
156 <param name="methods|minfrac" value="0.3"/>
157 <param name="methods|mzwid" value="0.01"/>
158 <param name="methods|density_options|option" value="show"/>
159 <param name="methods|density_options|max" value="50"/>
160 <conditional name="peaklist">
161 <param name="convertRTMinute" value="false" />
162 <param name="peaklistBool" value="true" />
163 <param name="numDigitsMZ" value="4" />
164 <param name="numDigitsRT" value="1" />
165 </conditional>
166 <output name="log">
167 <assert_contents>
168 <has_text text="object with 4 samples" />
169 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
170 <has_text text="Mass range: 200.1-600 m/z" />
171 <has_text text="Peaks: 9251 (about 2313 per sample)" />
172 <has_text text="Peak Groups: 8275" />
173 <has_text text="Sample classes: KO, WT" />
174 </assert_contents>
175 </output>
176 <output name="variableMetadata" file="faahKO.xset.group.variableMetadata.tsv" />
177 <output name="dataMatrix" file="faahKO.xset.group.dataMatrix.tsv" />
178 </test>
179 <test>
180 <param name="image" value="faahKO-single.xset.merged.RData"/>
181 <param name="methods|method" value="density"/>
182 <param name="methods|bw" value="5"/>
183 <param name="methods|minfrac" value="0.3"/>
184 <param name="methods|mzwid" value="0.01"/>
185 <param name="methods|density_options|option" value="show"/>
186 <param name="methods|density_options|max" value="50"/>
187 <output name="log">
188 <assert_contents>
189 <has_text text="object with 4 samples" />
190 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
191 <has_text text="Mass range: 200.1-600 m/z" />
192 <has_text text="Peaks: 9251 (about 2313 per sample)" />
193 <has_text text="Peak Groups: 664" />
194 <has_text text="Sample classes: ." />
195 </assert_contents>
196 </output>
197 </test>
198 <test>
199 <param name="image" value="MM-single.xset.merged.RData"/>
200 <param name="methods|method" value="density"/>
201 <param name="methods|bw" value="5"/>
202 <param name="methods|minfrac" value="0.3"/>
203 <param name="methods|mzwid" value="0.01"/>
204 <param name="methods|density_options|option" value="show"/>
205 <param name="methods|density_options|max" value="50"/>
206 <output name="log">
207 <assert_contents>
208 <has_text text="object with 2 samples" />
209 <has_text text="Time range: 19.7-307.3 seconds (0.3-5.1 minutes)" />
210 <has_text text="Mass range: 117.0357-936.7059 m/z" />
211 <has_text text="Peaks: 236 (about 118 per sample)" />
212 <has_text text="Peak Groups: 236" />
213 <has_text text="Sample classes: ." />
214 </assert_contents>
215 </output>
138 </test> 216 </test>
139 <!--<test> 217 <!--<test>
140 <param name="image" value="xset.group.retcor.RData"/> 218 <param name="image" value="xset.group.retcor.RData"/>
141 <param name="methods|method" value="density"/> 219 <param name="methods|method" value="density"/>
142 <param name="methods|bw" value="5"/> 220 <param name="methods|bw" value="5"/>
172 <has_text text="Peak Groups: 8157" /> 250 <has_text text="Peak Groups: 8157" />
173 <has_text text="Sample classes: KO, WT" /> 251 <has_text text="Sample classes: KO, WT" />
174 </assert_contents> 252 </assert_contents>
175 </output> 253 </output>
176 </test> 254 </test>
255 <test>
256 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
257 <param name="methods|method" value="density"/>
258 <param name="methods|bw" value="5"/>
259 <param name="methods|minfrac" value="0.3"/>
260 <param name="methods|mzwid" value="0.01"/>
261 <param name="methods|density_options|option" value="show"/>
262 <param name="methods|density_options|max" value="50"/>
263 <output name="log">
264 <assert_contents>
265 <has_text text="object with 4 samples" />
266 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
267 <has_text text="Mass range: 200.1-600 m/z" />
268 <has_text text="Peaks: 9251 (about 2313 per sample)" />
269 <has_text text="Peak Groups: 8157" />
270 <has_text text="Sample classes: KO, WT" />
271 </assert_contents>
272 </output>
273 </test>
177 </tests> 274 </tests>
178 275
179 <help><![CDATA[ 276 <help><![CDATA[
180 277
181 @HELP_AUTHORS@ 278 @HELP_AUTHORS@
182 279
183 ========== 280 ==========
184 Xcms.Group 281 Xcms.Group
185 ========== 282 ==========
200 297
201 ========================= ================= =================== ========== 298 ========================= ================= =================== ==========
202 Name output file format parameter 299 Name output file format parameter
203 ========================= ================= =================== ========== 300 ========================= ================= =================== ==========
204 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 301 xcms.xcmsSet xset.RData rdata.xcms.raw RData file
302 ------------------------- ----------------- ------------------- ----------
303 xcms.xcmsSet Merger xset.RData rdata.xcms.raw RData file
205 ------------------------- ----------------- ------------------- ---------- 304 ------------------------- ----------------- ------------------- ----------
206 xcms.retcor xset.RData rdata.xcms.retcor RData file 305 xcms.retcor xset.RData rdata.xcms.retcor RData file
207 ========================= ================= =================== ========== 306 ========================= ================= =================== ==========
208 307
209 308
229 ----------- 328 -----------
230 329
231 +---------------------------+-----------------------+ 330 +---------------------------+-----------------------+
232 | Parameter : num + label | Format | 331 | Parameter : num + label | Format |
233 +===========================+=======================+ 332 +===========================+=======================+
234 | 1 : RData file | rdata.xcms.group | 333 | Or : RData file | rdata.xcms.raw |
334 +---------------------------+-----------------------+
335 | Or : RData file | rdata.xcms.retcor |
235 +---------------------------+-----------------------+ 336 +---------------------------+-----------------------+
236 337
237 338
238 ---------- 339 ----------
239 Parameters 340 Parameters
262 xset.group.Rplots.pdf 363 xset.group.Rplots.pdf
263 364
264 xset.group.RData: rdata.xcms.group format 365 xset.group.RData: rdata.xcms.group format
265 366
266 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). 367 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
267 368
268 369
269 ------ 370 ------
270 371
271 .. class:: infomark 372 .. class:: infomark
272 373
273 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool. 374 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.
274 375
275 376
276 --------------------------------------------------- 377 ---------------------------------------------------
277 378
278 379
279 --------------- 380 ---------------
280 Working example 381 Working example
310 --------------------------------------------------- 411 ---------------------------------------------------
311 412
312 Changelog/News 413 Changelog/News
313 -------------- 414 --------------
314 415
416 **Version 2.1.0 - 07/02/2017**
417
418 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate
419
420 - IMPROVEMENT: xcms.group can deal with merged individual data from "xcms.xcmsSet Merger"
421
422 - BUGFIX: the default value of "density" -> "Maximum number of groups to identify in a single m/z slice" which was of 5 have been changed to fix with the XMCS default values to 50
423
315 **Version 2.0.6 - 06/07/2016** 424 **Version 2.0.6 - 06/07/2016**
316 425
317 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 426 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
318 427
319 **Version 2.0.5 - 04/04/2016** 428 **Version 2.0.5 - 04/04/2016**
320 429
321 - TEST: refactoring to pass planemo test using conda dependencies 430 - TEST: refactoring to pass planemo test using conda dependencies
322 431
323 432
324 **Version 2.0.4 - 10/02/2016** 433 **Version 2.0.4 - 10/02/2016**
325 434
326 - BUGFIX: better management of errors. Datasets remained green although the process failed 435 - BUGFIX: better management of errors. Datasets remained green although the process failed