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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 2f3f29dbaaa8568b40818d3476159c384f1a21d6-dirty"
author eschen42
date Fri, 12 Feb 2021 18:05:29 +0000
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1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy1">
2
3 <description>Remove or merge chromatographic peaks based on specific criteria.</description>
4
5 <macros>
6 <import>macros.xml</import>
7 <import>macros_xcms.xml</import>
8 </macros>
9
10 <requirements>
11 <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
12 <requirement type="package" version="1.1_5">r-batch</requirement>
13 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
14 <requirement type="package" version="6.0">unzip</requirement>
15 </requirements>
16
17 <expand macro="stdio"/>
18
19 <command><![CDATA[
20 @COMMAND_RSCRIPT@/xcms_refine.r
21 image '$image'
22
23 method $methods.method
24 #if $methods.method == "CleanPeaks":
25 maxPeakwidth $methods.maxPeakwidth
26 #elif $methods.method == "FilterIntensity":
27 threshold $methods.threshold
28 nValues $methods.nValues
29 value $methods.value
30 #else:
31 expandRt $methods.expandRt
32 expandMz $methods.expandMz
33 ppm $methods.ppm
34 minProp $methods.minProp
35 #end if
36
37 msLevel $msLevel
38
39 @COMMAND_FILE_LOAD@
40
41 @COMMAND_LOG_EXIT@
42 ]]></command>
43
44 <inputs>
45 <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
46 <conditional name="methods">
47 <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
48 <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
49 <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
50 <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
51 </param>
52 <when value="CleanPeaks">
53 <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds" />
54 </when>
55 <when value="FilterIntensity">
56 <param argument="threshold" type="float" value="0" label="minimal required intensity" help="minimal required intensity for a peak to be retained. Defaults to 0.0." />
57 <param argument="nValues" type="integer" value="1" label="minimum number of data points per peak" help="number of data points (per chromatographic peak) that have to be >= threshold. Defaults to 1." />
58 <param argument="value" type="text" value="maxo" label="chromatographic intensity type ('intb', 'into', or 'maxo')" help="intensity type (which must be set in the chromatographic peaks input data) that should be used for the filtering. Defaults 'maxo'." />
59 <param name="value" type="select" label="Definition of peak intensity" help="See the manual. 'intb' requires centWave processed data">
60 <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
61 <option value="into">into - use integrated peak intensities</option>
62 <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
63 </param>
64 </when>
65 <when value="MergeNeighboringPeaks">
66 <param argument="expandRt" type="float" value="2" label="rt expansion (seconds)" help="seconds of expansion of retention time window (on both sides) to check for overlapping peaks. Defaults to 2." />
67 <param argument="expandMz" type="float" value="0" label="m/z expansion (m/z units)" help="'m/z units' of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 0." />
68 <param argument="ppm" type="float" value="10" label="ppm expansion (ppm units)" help="'relative 'm/z units' (in parts per million) of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 10." />
69 <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual. Minimum proportion midway between peaks relative to the smaller peak's 'maxo' (maximal intensity at peak apex). Defaults to 0.75." />
70 </when>
71 </conditional>
72 <param argument="msLevel" type="integer" value="1" label="msLevel for refinement" help="the MS level on which refinement should be performed. Defaults to 1." />
73
74 <expand macro="input_file_load"/>
75 </inputs>
76
77 <outputs>
78 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
79 </outputs>
80
81 <tests>
82 <!--
83 test 1 - MergeNeighboringPeaks method
84 -->
85 <test>
86 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
87 <conditional name="methods">
88 <param name="method" value="MergeNeighboringPeaks"/>
89 <param name="expandRt" value="2" />
90 <param name="expandMz" value="0" />
91 <param name="ppm" value="10" />
92 <param name="minProp" value="0.75" />
93 </conditional>
94 <expand macro="test_file_load_single"/>
95 <assert_stderr>
96 <has_text text="Evaluating 547 peaks in file wt15.CDF for merging ... OK" />
97 <has_text text="Evaluating 547 peaks in file wt16.CDF for merging ... OK" />
98 <has_text text="Evaluating 558 peaks in file ko15.CDF for merging ... OK"/>
99 <has_text text="Evaluating 589 peaks in file ko16.CDF for merging ... OK" />
100 <has_text text="Merging reduced 9251 chromPeaks to 9093" />
101 </assert_stderr>
102 <assert_stdout>
103 <has_text text="object with 4 samples" />
104 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
105 <has_text text="Mass range: 200.1-600 m/z" />
106 <has_text text="Peaks: 9093 (about 2273 per sample)" />
107 </assert_stdout>
108 </test>
109 <!--
110 test 2 - FilterIntensity method
111 -->
112 <test>
113 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
114 <conditional name="methods">
115 <param name="method" value="FilterIntensity"/>
116 <param name="threshold" value="1e5" />
117 <param name="nValues" value="3" />
118 <param name="value" value="into" />
119 </conditional>
120 <expand macro="test_file_load_single"/>
121 <assert_stderr>
122 <has_text text="Removed 9018 chromatographic peaks" />
123 </assert_stderr>
124 <assert_stdout>
125 <has_text text="object with 4 samples" />
126 <has_text text="Time range: 2657.9-4124.2 seconds (44.3-68.7 minutes)" />
127 <has_text text="Mass range: 256.1-599.4 m/z" />
128 <has_text text="Peaks: 233 (about 58 per sample)" />
129 </assert_stdout>
130 </test>
131 <!--
132 test 3 - CleanPeaks method
133 -->
134 <test>
135 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
136 <conditional name="methods">
137 <param name="method" value="CleanPeaks"/>
138 <param name="maxPeakwidth" value="8" />
139 </conditional>
140 <expand macro="test_file_load_single"/>
141 <assert_stderr>
142 <has_text text="Removed 6037 of 9251 chromatographic peaks" />
143 </assert_stderr>
144 <assert_stdout>
145 <has_text text="object with 4 samples" />
146 <has_text text="Time range: 2524.9-4473.2 seconds (42.1-74.6 minutes)" />
147 <has_text text="Mass range: 200.2-600 m/z" />
148 <has_text text="Peaks: 3214 (about 804 per sample)" />
149 </assert_stdout>
150 </test>
151 </tests>
152
153 <help><![CDATA[
154
155 .. class:: infomark
156
157 **Authors** Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it
158
159 @HELP_AUTHORS_WRAPPERS@
160
161 ---------------------------------------------------
162
163
164 =====================
165 xcms refineChromPeaks
166 =====================
167
168 -----------
169 Description
170 -----------
171
172 After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
173 It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.
174
175 Note well that refineChromPeaks methods will always remove feature definitions,
176 because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
177 Therefore it must only be run immediately after findChromPeaks (xcmsSet).
178
179 -----------------
180 Workflow position
181 -----------------
182
183 **Upstream tools**
184
185 ==================================== ======================== ==============================
186 Name Output file Format
187 ==================================== ======================== ==============================
188 xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks
189 ------------------------------------ ------------------------ ------------------------------
190 xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
191 ==================================== ======================== ==============================
192
193
194 **Downstream tools**
195
196 ==================================== ======================== =========================
197 Name Output file Format
198 ==================================== ======================== =========================
199 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
200 ------------------------------------ ------------------------ -------------------------
201 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
202 ==================================== ======================== =========================
203
204 **General schema of the metabolomic workflow**
205
206 This tool would appear between findChromPeaks and group, but only when the choice of peaks needs to be refined, e.g., to accommodate HILIC data.
207
208 ---------------------------------------------------
209
210 ----------
211 Parameters
212 ----------
213
214 Method to use for refinement
215 ----------------------------
216
217 **CleanPeaks**
218
219 | Remove chromatographic peaks with too large rt width.
220 | See the CleanPeaks_manual_
221
222 **FilterIntensity**
223
224 | Remove chromatographic peaks based on intensity.
225 | See the FilterIntensity_manual_
226
227 **MergeNeighboringPeaks**
228
229 | Merge neighboring and overlapping chromatographic peaks.
230 | See the MergeNeighboringPeaks_manual_
231
232 .. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
233 .. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
234 .. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html
235
236 @HELP_XCMS_MANUAL@
237
238 ------------
239 Output files
240 ------------
241
242 xset.RData: rdata.xcms.findchrompeaks format
243
244 | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
245 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
246
247
248 ---------------------------------------------------
249
250 Changelog/News
251 --------------
252
253 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
254
255
256 **Version 3.6.1.0 - 08/02/2021**
257
258 - NEW: first version of tool wrapper
259
260
261 ]]></help>
262
263 <citations>
264 <citation type="doi">10.5281/zenodo.3909299</citation>
265 <expand macro="citation_w4m"/>
266 <citation type="doi">10.1021/ac051437y</citation>
267 </citations>
268
269
270 </tool>