Mercurial > repos > workflow4metabolomics > xcms_refine

comparison abims_xcms_refine.xml @ 0:eb115eb8f25c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
author workflow4metabolomics
date Thu, 17 Jun 2021 07:42:55 +0000
parents
children 20f8ebc3a391
comparison
equal deleted inserted replaced
-1:000000000000 0:eb115eb8f25c
1 <tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0">
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 <expand macro="requirements"/>
11
12 <expand macro="stdio"/>
13
14 <command><![CDATA[
15 @COMMAND_RSCRIPT@/xcms_refine.r
16 image '$image'
17
18 method $methods.method
19 #if $methods.method == "CleanPeaks":
20 maxPeakwidth $methods.maxPeakwidth
21 #elif $methods.method == "FilterIntensity":
22 threshold $methods.threshold
23 nValues $methods.nValues
24 value $methods.value
25 #else:
26 expandRt $methods.expandRt
27 expandMz $methods.expandMz
28 ppm $methods.ppm
29 minProp $methods.minProp
30 #end if
31
32 msLevel $msLevel
33
34 @COMMAND_FILE_LOAD@
35
36 @COMMAND_LOG_EXIT@
37 ]]></command>
38
39 <inputs>
40 <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
41 <conditional name="methods">
42 <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
43 <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
44 <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
45 <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
46 </param>
47 <when value="CleanPeaks">
48 <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds. See CleanPeaks manual (linked in help below)." />
49 </when>
50 <when value="FilterIntensity">
51 <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." />
52 <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." />
53 <param name="value" type="select" label="Definition of peak intensity" help="See the FilterIntensity manual (linked in help below). 'intb' requires centWave processed data">
54 <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
55 <option value="into">into - use integrated peak intensities</option>
56 <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
57 </param>
58 </when>
59 <when value="MergeNeighboringPeaks">
60 <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." />
61 <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." />
62 <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." />
63 <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual (linked in help below). Minimum proportion midway between peaks relative to the smaller peak's 'maxo' (maximal intensity at peak apex). Defaults to 0.75." />
64 </when>
65 </conditional>
66 <param argument="msLevel" type="integer" value="1" label="msLevel for refinement" help="the MS level on which refinement should be performed. Defaults to 1." />
67
68 <expand macro="input_file_load"/>
69 </inputs>
70
71 <outputs>
72 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
73 </outputs>
74
75 <tests>
76 <!--
77 test 1 - MergeNeighboringPeaks method
78 -->
79 <test>
80 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
81 <conditional name="methods">
82 <param name="method" value="MergeNeighboringPeaks"/>
83 <param name="expandRt" value="2" />
84 <param name="expandMz" value="0" />
85 <param name="ppm" value="10" />
86 <param name="minProp" value="0.75" />
87 </conditional>
88 <expand macro="test_file_load_single"/>
89 <assert_stderr>
90 <has_text text="Evaluating 547 peaks in file wt15.CDF for merging ... OK" />
91 <has_text text="Evaluating 547 peaks in file wt16.CDF for merging ... OK" />
92 <has_text text="Evaluating 558 peaks in file ko15.CDF for merging ... OK"/>
93 <has_text text="Evaluating 589 peaks in file ko16.CDF for merging ... OK" />
94 <has_text text="Merging reduced 9251 chromPeaks to 9093" />
95 </assert_stderr>
96 <assert_stdout>
97 <has_text text="object with 4 samples" />
98 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
99 <has_text text="Mass range: 200.1-600 m/z" />
100 <has_text text="Peaks: 9093 (about 2273 per sample)" />
101 </assert_stdout>
102 </test>
103 <!--
104 test 2 - FilterIntensity method
105 -->
106 <test>
107 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
108 <conditional name="methods">
109 <param name="method" value="FilterIntensity"/>
110 <param name="threshold" value="1e5" />
111 <param name="nValues" value="3" />
112 <param name="value" value="into" />
113 </conditional>
114 <expand macro="test_file_load_single"/>
115 <assert_stderr>
116 <has_text text="Removed 9018 chromatographic peaks" />
117 </assert_stderr>
118 <assert_stdout>
119 <has_text text="object with 4 samples" />
120 <has_text text="Time range: 2657.9-4124.2 seconds (44.3-68.7 minutes)" />
121 <has_text text="Mass range: 256.1-599.4 m/z" />
122 <has_text text="Peaks: 233 (about 58 per sample)" />
123 </assert_stdout>
124 </test>
125 <!--
126 test 3 - CleanPeaks method
127 -->
128 <test>
129 <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
130 <conditional name="methods">
131 <param name="method" value="CleanPeaks"/>
132 <param name="maxPeakwidth" value="8" />
133 </conditional>
134 <expand macro="test_file_load_single"/>
135 <assert_stderr>
136 <has_text text="Removed 6037 of 9251 chromatographic peaks" />
137 </assert_stderr>
138 <assert_stdout>
139 <has_text text="object with 4 samples" />
140 <has_text text="Time range: 2524.9-4473.2 seconds (42.1-74.6 minutes)" />
141 <has_text text="Mass range: 200.2-600 m/z" />
142 <has_text text="Peaks: 3214 (about 804 per sample)" />
143 </assert_stdout>
144 </test>
145 </tests>
146
147 <help><![CDATA[
148
149 .. class:: infomark
150
151 **Authors** Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it
152
153 @HELP_AUTHORS_WRAPPERS@
154
155 ---------------------------------------------------
156
157
158 =====================
159 xcms refineChromPeaks
160 =====================
161
162 -----------
163 Description
164 -----------
165
166 After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
167 It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.
168
169 Note well that refineChromPeaks methods will always remove feature definitions,
170 because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
171 Therefore it must only be run immediately after findChromPeaks (xcmsSet).
172
173 -----------------
174 Workflow position
175 -----------------
176
177 **Upstream tools**
178
179 ==================================== ======================== ==============================
180 Name Output file Format
181 ==================================== ======================== ==============================
182 xcms.findChromPeaks Merger (single) xset.merged.RData rdata.xcms.findchrompeaks
183 ------------------------------------ ------------------------ ------------------------------
184 xcms.findChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
185 ==================================== ======================== ==============================
186
187
188 **Downstream tools**
189
190 ==================================== ======================== =========================
191 Name Output file Format
192 ==================================== ======================== =========================
193 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
194 ------------------------------------ ------------------------ -------------------------
195 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
196 ==================================== ======================== =========================
197
198 **General schema of the metabolomic workflow**
199
200 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.
201
202 ---------------------------------------------------
203
204 ----------
205 Parameters
206 ----------
207
208 Method to use for refinement
209 ----------------------------
210
211 **CleanPeaks**
212
213 | Remove chromatographic peaks with too large rt width.
214 | See the CleanPeaks_manual_
215
216 **FilterIntensity**
217
218 | Remove chromatographic peaks based on intensity.
219 | See the FilterIntensity_manual_
220
221 **MergeNeighboringPeaks**
222
223 | Merge neighboring and overlapping chromatographic peaks.
224 | See the MergeNeighboringPeaks_manual_
225
226 .. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
227 .. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
228 .. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html
229
230 @HELP_XCMS_MANUAL@
231
232 ------------
233 Output files
234 ------------
235
236 xset.RData: rdata.xcms.findchrompeaks format
237
238 | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
239 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
240
241
242 ---------------------------------------------------
243
244 Changelog/News
245 --------------
246
247 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
248
249
250 **Version 3.6.1.0 - 08/02/2021**
251
252 - NEW: first version of tool wrapper
253
254
255 ]]></help>
256
257 <citations>
258 <citation type="doi">10.5281/zenodo.3909299</citation>
259 <expand macro="citation_w4m"/>
260 <citation type="doi">10.1021/ac051437y</citation>
261 </citations>
262
263
264 </tool>