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comparison abims_xcms_retcor.xml @ 10:8828cba9aedd draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:12:29 -0400
parents e4e0254a3c0a
children 950b97b679c6
comparison
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9:e4e0254a3c0a 10:8828cba9aedd
1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.1"> 1 <tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@WRAPPER_VERSION@.0">
2 2
3 <description>Retention Time Correction using retcor function from xcms R package </description> 3 <description>Retention Time Correction</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <import>macros_xcms.xml</import>
7 </macros> 8 </macros>
8 9
9 <expand macro="requirements"/> 10 <expand macro="requirements"/>
10 <expand macro="stdio"/> 11 <expand macro="stdio"/>
11 12
12 <command><![CDATA[ 13 <command><![CDATA[
13 @COMMAND_XCMS_SCRIPT@ 14 @COMMAND_RSCRIPT@/xcms_retcor.r
14 image '$image' 15 image '$image'
15 xfunction retcor
16
17 xsetRdataOutput '$xsetRData'
18 ticspdf '$ticsCorPdf'
19 bicspdf '$bpcsCorPdf'
20 rplotspdf '$rplotsPdf'
21 16
22 method $methods.method 17 method $methods.method
23 #if $methods.method == "obiwarp": 18 #if $methods.method == "PeakGroups":
24 profStep $methods.profStep 19 minFraction $methods.minFraction
20 extraPeaks $methods.extraPeaks
21 smooth $methods.smooth_cond.smooth
22 ## PeakGroupsSmoothLoess Advanced
23 span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span
24 family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family
25 #else 25 #else
26 smooth $methods.smooth 26 binSize $methods.binSize
27 extra $methods.extra 27 ## Advanced
28 missing $methods.missing 28 #if $methods.ObiwarpAdv.centerSample != "":
29 #if $methods.options.option == "show": 29 centerSample $methods.ObiwarpAdv.centerSample
30 span $methods.options.span
31 family $methods.options.family
32 plottype $methods.options.plottype
33 #end if 30 #end if
31 response $methods.ObiwarpAdv.response
32 distFun $methods.ObiwarpAdv.distFunCond.distFun
33 gapInit $methods.ObiwarpAdv.distFunCond.gapInit
34 gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend
35 factorDiag $methods.ObiwarpAdv.factorDiag
36 factorGap $methods.ObiwarpAdv.factorGap
37 localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment
38 initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty
34 #end if 39 #end if
35 40
36 @COMMAND_FILE_LOAD@ 41 @COMMAND_FILE_LOAD@
37 42
38 @COMMAND_LOG_EXIT@ 43 @COMMAND_LOG_EXIT@
39 ]]></command> 44 ]]></command>
40 45
41 <inputs> 46 <inputs>
42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> 47 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
43 <conditional name="methods"> 48 <conditional name="methods">
44 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > 49 <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
45 <option value="obiwarp" >obiwarp</option> 50 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
46 <option value="peakgroups" selected="true">peakgroups</option> 51 <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>
47 </param> 52 </param>
48 <when value="obiwarp"> 53 <when value="PeakGroups">
49 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> 54 <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/>
50 </when> 55 <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction" help="For a data set with 6 samples, ‘extraPeaks = 1’ uses all peak groups with a total peak count lower or equal to ‘6 + 1’. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" />
51 <when value="peakgroups"> 56 <conditional name="smooth_cond">
52 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" > 57 <param argument="smooth" type="select" label="Smooth method" >
53 <option value="loess">loess</option> 58 <option value="loess" selected="true">loess - non-linear alignment</option>
54 <option value="linear">linear</option> 59 <option value="linear">linear - linear alignment</option>
55 </param>
56 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
57 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
58
59 <conditional name="options">
60 <param name="option" type="select" label="Advanced options">
61 <option value="show">show</option>
62 <option value="hide" selected="true">hide</option>
63 </param> 60 </param>
64 <when value="show"> 61 <when value="loess">
65 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> 62 <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">
66 63 <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />
67 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> 64 <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
68 <option value="gaussian" selected="true">gaussian</option> 65 <option value="gaussian" selected="true">gaussian</option>
69 <option value="symmetric">symmetric</option> 66 <option value="symmetric">symmetric</option>
70 </param> 67 </param>
71 68 </section>
72 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
73 <option value="none" selected="true">none</option>
74 <option value="deviation">deviation</option>
75 <option value="mdevden">mdevden</option>
76 </param>
77
78 </when> 69 </when>
79 <when value="hide"> 70 <when value="linear" />
80 </when>
81 </conditional> 71 </conditional>
82 </when> 72 </when>
73 <when value="Obiwarp">
74 <param argument="binSize" type="float" value="1" label="Bin size (in mz dimension) to be used for the profile matrix generation" help="See ‘step’ parameter in ‘profile-matrix’ documentation for more details. (previously profStep)" />
75 <section name="ObiwarpAdv" title="Advanced Options" expanded="False">
76 <param argument="centerSample" type="integer" value="" optional="true" label="Index of the center sample in the experiment" help="It defaults to ‘floor(median(1:length(fileNames(object))))’" />
77 <param argument="response" type="integer" value="1" label="Defining the responsiveness of warping" help="with ‘response = 0’ giving linear warping on start and end points and ‘response = 100’ warping using all bijective anchors." />
78 <conditional name="distFunCond">
79 <param argument="distFun" type="select" label="Distance function to be used">
80 <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option>
81 <option value="cor">cor - Pearson's correlation</option>
82 <option value="cov">cov - covariance</option>
83 <option value="prd">prd - product</option>
84 <option value="euc">euc - Euclidian distance</option>
85 </param>
86 <when value="cor_opt">
87 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
88 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
89 </when>
90 <when value="cor">
91 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
92 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
93 </when>
94 <when value="cov">
95 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
96 <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" />
97 </when>
98 <when value="prd">
99 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
100 <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" />
101 </when>
102 <when value="euc">
103 <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" />
104 <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" />
105 </when>
106 </conditional>
107 <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" />
108 <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" />
109 <conditional name="localAlignmentCond">
110 <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment">
111 <option value="FALSE" selected="true">FALSE</option>
112 <option value="TRUE">TRUE</option>
113 </param>
114 <when value="FALSE">
115 <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" />
116 </when>
117 <when value="TRUE">
118 <param argument="initPenalty" type="float" value="0" label="Penalty for initiating an alignment" />
119 </when>
120 </conditional>
121 </section>
122 </when>
83 </conditional> 123 </conditional>
84 124
85 <expand macro="input_file_load"/> 125 <expand macro="input_file_load"/>
86 126
87 </inputs> 127 </inputs>
88 128
89 <outputs> 129 <outputs>
90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> 130 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.adjustRtime.RData" from_work_dir="retcor.RData" />
91 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> 131 <data name="rawVSadjustedPdf" format="pdf" label="${image.name[:-6]}_rawVSadjusted.adjustRtime.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
92 <filter>(methods['method'] == 'peakgroups')</filter>
93 <filter>(options['option'] == 'show')</filter>
94 <filter>(family == 'symmetric')</filter>
95 <filter>(plottype != 'none')</filter>
96 </data>
97 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
98 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
99 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
100 </outputs> 132 </outputs>
101 133
102 <tests> 134 <tests>
103 <!--<test>
104 <param name="image" value="xset.group.RData"/>
105 <param name="methods|method" value="peakgroups"/>
106 <param name="methods|smooth" value="loess"/>
107 <param name="methods|extra" value="1"/>
108 <param name="methods|missing" value="1"/>
109 <param name="methods|options|option" value="show"/>
110 <param name="methods|options|span" value="0.2"/>
111 <param name="methods|options|family" value="gaussian"/>
112 <param name="methods|options|plottype" value="deviation"/>
113 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
114 <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
115 <output name="log">
116 <assert_contents>
117 <has_text text="object with 4 samples" />
118 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
119 <has_text text="Mass range: 50.0021-999.9863 m/z" />
120 <has_text text="Peaks: 59359 (about 14840 per sample)" />
121 <has_text text="Peak Groups: 0" />
122 <has_text text="Sample classes: bio, blank" />
123 </assert_contents>
124 </output>
125 </test>-->
126 <test> 135 <test>
127 <param name="image" value="faahKO.xset.group.RData"/> 136 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
128 <param name="methods|method" value="peakgroups"/> 137 <conditional name="methods">
129 <param name="methods|smooth" value="loess"/> 138 <param name="method" value="PeakGroups"/>
130 <param name="methods|extra" value="1"/> 139 <param name="extraPeaks" value="1"/>
131 <param name="methods|missing" value="1"/> 140 <param name="minFraction" value="1"/>
132 <param name="methods|options|option" value="show"/> 141 <conditional name="smooth_cond">
133 <param name="methods|options|span" value="0.2"/> 142 <param name="smooth" value="loess"/>
134 <param name="methods|options|family" value="gaussian"/> 143 <section name="PeakGroupsSmoothLoessAdv">
135 <param name="methods|options|plottype" value="deviation"/> 144 <param name="span" value="0.2"/>
145 <param name="family" value="gaussian"/>
146 </section>
147 </conditional>
148 </conditional>
149 <expand macro="test_file_load_single"/>
150 <assert_stdout>
151 <has_text text="extraPeaks: 1" />
152 <has_text text="minFraction: 1" />
153 <has_text text="span: 0.2" />
154 <has_text text="object with 4 samples" />
155 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
156 <has_text text="Mass range: 200.1-600 m/z" />
157 <has_text text="Peaks: 9251 (about 2313 per sample)" />
158 <has_text text="Peak Groups: 0" />
159 <has_text text="Sample classes: KO, WT" />
160 </assert_stdout>
161 </test>
162 <!-- DISABLE FOR TRAVIS : Zip
163 <test>
164 <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/>
165 <conditional name="methods">
166 <param name="method" value="PeakGroups"/>
167 <param name="extraPeaks" value="1"/>
168 <param name="minFraction" value="1"/>
169 <conditional name="smooth_cond">
170 <param name="smooth" value="loess"/>
171 <section name="PeakGroupsSmoothLoessAdv">
172 <param name="span" value="0.2"/>
173 <param name="family" value="gaussian"/>
174 </section>
175 </conditional>
176 </conditional>
136 <expand macro="test_file_load_zip"/> 177 <expand macro="test_file_load_zip"/>
137 <output name="log"> 178 <assert_stdout>
138 <assert_contents> 179 <has_text text="object with 4 samples" />
139 <has_text text="object with 4 samples" /> 180 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
140 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> 181 <has_text text="Mass range: 200.1-600 m/z" />
141 <has_text text="Mass range: 200.1-600 m/z" /> 182 <has_text text="Peaks: 9251 (about 2313 per sample)" />
142 <has_text text="Peaks: 9251 (about 2313 per sample)" /> 183 <has_text text="Peak Groups: 0" />
143 <has_text text="Peak Groups: 0" /> 184 <has_text text="Sample classes: KO, WT" />
144 <has_text text="Sample classes: KO, WT" /> 185 </assert_stdout>
145 </assert_contents>
146 </output>
147 </test> 186 </test>
187 -->
188 <!-- DISABLE FOR TRAVIS
189 Test to test the different methods parameters
148 <test> 190 <test>
149 <param name="image" value="faahKO-single-class.xset.group.RData"/> 191 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
150 <param name="methods|method" value="peakgroups"/> 192 <conditional name="methods">
151 <param name="methods|smooth" value="loess"/> 193 <param name="method" value="Obiwarp"/>
152 <param name="methods|extra" value="1"/> 194 <section name="ObiwarpAdv">
153 <param name="methods|missing" value="1"/> 195 <param name="centerSample" value="1"/>
154 <param name="methods|options|option" value="show"/> 196 <param name="response" value="0"/>
155 <param name="methods|options|span" value="0.2"/> 197 <conditional name="distFunCond">
156 <param name="methods|options|family" value="gaussian"/> 198 <param name="distFun" value="cov"/>
157 <param name="methods|options|plottype" value="deviation"/> 199 <param name="gapInit" value="0.1" />
200 </conditional>
201 </section>
202 </conditional>
158 <expand macro="test_file_load_single"/> 203 <expand macro="test_file_load_single"/>
159 <output name="log"> 204 <assert_stdout>
160 <assert_contents> 205 <has_text text="centerSample: 1" />
161 <has_text text="object with 4 samples" /> 206 <has_text text="response: 0" />
162 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> 207 <has_text text="distFun: cov" />
163 <has_text text="Mass range: 200.1-600 m/z" /> 208 <has_text text="gapInit: 0.1" />
164 <has_text text="Peaks: 9251 (about 2313 per sample)" /> 209 <has_text text="gapExtend: 11.7" />
165 <has_text text="Peak Groups: 0" /> 210 </assert_stdout>
166 <has_text text="Sample classes: KO, WT" />
167 </assert_contents>
168 </output>
169 </test> 211 </test>
212 -->
170 </tests> 213 </tests>
171 214
172 <help><![CDATA[ 215 <help><![CDATA[
173 216
174 @HELP_AUTHORS@ 217 @HELP_AUTHORS@
175 218
176 =========== 219 ================
177 Xcms.retcor 220 xcms adjustRtime
178 =========== 221 ================
179 222
180 ----------- 223 -----------
181 Description 224 Description
182 ----------- 225 -----------
183 226
189 fraction of samples and thus provide an incomplete picture of the drift at that time point. 232 fraction of samples and thus provide an incomplete picture of the drift at that time point.
190 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping. 233 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
191 234
192 .. class:: warningmark 235 .. class:: warningmark
193 236
194 **After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is 237 **After an adjustRtime step, it is mandatory to do a groupChromPeaks step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
195 discarded)** 238 discarded)**
196 239
197 240
198 241
199 ----------------- 242 -----------------
201 ----------------- 244 -----------------
202 245
203 246
204 **Upstream tools** 247 **Upstream tools**
205 248
206 ========================= ================= ======= ========== 249 ========================= ============================ ==============================
207 Name output file format parameter 250 Name Output file Format
208 ========================= ================= ======= ========== 251 ========================= ============================ ==============================
209 xcms.group xset.group.RData RData RData file 252 xcms.findChromPeaks raw.xset.RData rdata.xcms.findchrompeaks
210 ========================= ================= ======= ========== 253 ------------------------- ---------------------------- ------------------------------
254 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
255 ========================= ============================ ==============================
211 256
212 257
213 **Downstream tools** 258 **Downstream tools**
214 259
215 +---------------------------+------------------+--------+ 260 =========================== ============================ ================
216 | Name | Output file | Format | 261 Name Output file Format
217 +===========================+==================+========+ 262 =========================== ============================ ================
218 |xcms.group | xset.retcor.RData| RData | 263 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group
219 +---------------------------+------------------+--------+ 264 =========================== ============================ ================
220
221 The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
222 265
223 266
224 **General schema of the metabolomic workflow** 267 **General schema of the metabolomic workflow**
225 268
226 .. image:: xcms_retcor_workflow.png 269 .. image:: xcms_retcor_workflow.png
227 270
228 271 ---------------------------------------------------
229 -----------
230 Input files
231 -----------
232
233 +---------------------------+----------------------+
234 | Parameter : num + label | Format |
235 +===========================+======================+
236 | 1 : RData file | rdata.xcms.group |
237 +---------------------------+----------------------+
238
239 272
240 ---------- 273 ----------
241 Parameters 274 Parameters
242 ---------- 275 ----------
243 276
244 Method 277 Method
245 ------ 278 ------
246 279
247 **peakgroups** 280 **PeakGroups**
248 281
249 | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.) 282 | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample.
250 | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points. 283 | See the PeakGroups_manual_
251 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**. 284
252 285 **Obiwarp**
253 **obiwarp** 286
254 287 | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping.
255 | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets. 288 | See the Obiwarp_manual_
256 | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.** 289
257 290 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
291 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
292
293 @HELP_XCMS_MANUAL@
258 294
259 ------------ 295 ------------
260 Output files 296 Output files
261 ------------ 297 ------------
262 298
263 xset.group.retcor.TICs_corrected.pdf 299 xset.groupChromPeaks.adjustRtime.RData: rdata.xcms.retcor format
264 300
265 | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step. 301 | Rdata file that will be necessary in the **xcms.groupChromPeaks** step of the workflow.
266
267 xset.group.retcor.BPCs_corrected.pdf
268
269 | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
270
271 xset.group.retcor.RData: rdata.xcms.retcor format
272
273 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
274
275
276 ------
277
278 .. class:: infomark
279
280 The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
281
282
283 ---------------------------------------------------
284
285 ---------------
286 Working example
287 ---------------
288
289 Input files
290 -----------
291
292 | RData file -> **xset.group.RData**
293
294 Parameters
295 ----------
296
297 | Method: -> **peakgroups**
298 | smooth: -> **loess**
299 | extra: -> **1**
300 | missing -> **1**
301 | Advanced options: -> **show**
302 | span -> **0.2**
303 | family -> **gaussian**
304 | plottype -> **deviation**
305
306
307 Output files
308 ------------
309
310 | **1) xset.group.retcor.RData: RData file**
311
312 | **2) Example of an xset.group.retcor.TICs_corrected pdf file**
313
314 .. image:: xcms_retcor.png
315 302
316 303
317 --------------------------------------------------- 304 ---------------------------------------------------
318 305
319 Changelog/News 306 Changelog/News
320 -------------- 307 --------------
321 308
309 **Version 3.0.0.0 - 08/03/2018**
310
311 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
312
313 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
314
315 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
316
317 - CHANGE: removing of the TIC and BPC plots. You can now use the dedicated tool "xcms plot chromatogram"
318
319
322 **Version 2.1.1 - 29/11/2017** 320 **Version 2.1.1 - 29/11/2017**
323 321
324 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C 322 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
325 323
324
326 **Version 2.1.0 - 03/02/2017** 325 **Version 2.1.0 - 03/02/2017**
327 326
328 - IMPROVEMENT: xcms.retcor can deal with merged individual data 327 - IMPROVEMENT: xcms.retcor can deal with merged individual data
329 328
329
330 **Version 2.0.8 - 22/12/2016** 330 **Version 2.0.8 - 22/12/2016**
331 331
332 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph 332 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
333 333
334
334 **Version 2.0.7 - 06/07/2016** 335 **Version 2.0.7 - 06/07/2016**
335 336
336 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 337 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
337 338
339
338 **Version 2.0.6 - 04/04/2016** 340 **Version 2.0.6 - 04/04/2016**
339 341
340 - TEST: refactoring to pass planemo test using conda dependencies 342 - TEST: refactoring to pass planemo test using conda dependencies
341 343
342 344