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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
author recetox
date Mon, 13 Feb 2023 10:26:59 +0000
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1 <macros>
2
3 <token name="@GENERAL_HELP@">
4 General Information
5 ===================
6
7 Overview
8 --------
9
10 recetox-aplcms is a software package for peak detection in high resolution mass spectrometry (HRMS) data.
11 It supports reading .mzml files in raw profile mode and uses a bi-Gaussian chromatographic peak shape for feature detection and quantification.
12
13 recetox-aplcms is based on the apLCMS package developed by Tianwei Yu at Emory University - see the citations and the apLCMS section beneath.
14 This version includes various software updates and is actively developed and maintained on `GitHub`_.
15 Please submit eventual bug reports as `issues`_ on the repository.
16
17 .. _GitHub: https://github.com/RECETOX/recetox-aplcms
18 .. _issues: https://github.com/RECETOX/recetox-aplcms/issues/new
19
20
21 Workflow
22 --------
23
24 .. image:: https://raw.githubusercontent.com/RECETOX/galaxytools/aee0dd6cf6c05936269efe4337c50e27cc68e86b/tools/recetox_aplcms/images/scheme.png
25 :width: 2560
26 :height: 788
27 :scale: 40
28 :alt: A picture of a workflow diagram.
29
30 The individual steps of the recetox-aplcms package can be combined in 2 separate workflows processing HRMS data in an unsupervised manner or by including a-priori knowledge.
31 The workflows consist of the following building blocks:
32
33 (1) remove noise - denoise the raw data and extract the EIC
34 (2) generate feature table - group features in EIC into peaks using peak-shape model
35 (3) compute clusters - compute mz and rt clusters across samples
36 (4) compute template - find the template for rt correction
37 (5) correct time - correct the rt across samples using splines
38 (6) align features - align identical features across samples
39 (7) recover weaker signals - recover missed features in samples based on the aligned features
40 (8) merge known table - add known features to detected features table and vice versa
41
42 For detailed documentation on the individual steps please see the individual tool wrappers.
43
44
45 apLCMS (Original Reference)
46 ---------------------------
47
48 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
49 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
50 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
51 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
52 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
53 </token>
54
55 <token name="@REMOVE_NOISE_HELP@">
56 recetox-aplcms - remove noise
57 =============================
58
59 This tool is the first step of recetox-aplcms.
60 It removes noise from the raw data and performs a first clustering step of points with close m/z values into the extracted ion chromatograms (EICs).
61 Only peaks with a minimum elution length of `min_run` seconds are kept.
62
63 Example Output
64 --------------
65 The raw data points contained in the scans of the `mzml` file are filtered for noise and grouped into clusters based on m/z values.
66 See an example output in the table below. The `group_number` column indicates the cluster index.
67
68 +----------------------+-------------------+-----------------------+--------------------+
69 | mz | rt | intensity | group_number |
70 +======================+===================+=======================+====================+
71 | 70.01060119055192 | 350.58654 | 21178.330810546875 | 5 |
72 +----------------------+-------------------+-----------------------+--------------------+
73 | 70.02334120404554 | 130.175262 | 287869.5478515625 | 10 |
74 +----------------------+-------------------+-----------------------+--------------------+
75 | 70.0287408273165 | 134.801352 | 60883.15185546875 | 11 |
76 +----------------------+-------------------+-----------------------+--------------------+
77 | 70.02872416715464 | 183.991896 | 9201.574584960938 | 11 |
78 +----------------------+-------------------+-----------------------+--------------------+
79 | ... | ... | ... | ... |
80 +----------------------+-------------------+-----------------------+--------------------+
81 </token>
82
83 <token name="@GENERATE_FEATURE_TABLE_HELP@">
84 recetox-aplcms - generate feature table
85 =======================================
86 The second step in the recetox-aplcms workflow performing peak shape parameter estimation.
87
88 This tool takes the grouped features created with `recetox-aplcms-remove-noise` and computes the peak shape in `rt` domain and integrates the peak area.
89
90
91 Example Output
92 --------------
93 The output contains the `mz` and `rt` of the peaks as well as the standard deviation in both direction of the peak for the bi-gaussian peak shape.
94
95 +----------------------+-------------------+-----------------+-------------------+----------------------+
96 | mz | rt | sd1 | sd2 | area |
97 +======================+===================+=================+===================+======================+
98 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.24595184 |
99 +----------------------+-------------------+-----------------+-------------------+----------------------+
100 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 |
101 +----------------------+-------------------+-----------------+-------------------+----------------------+
102 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.50659719 |
103 +----------------------+-------------------+-----------------+-------------------+----------------------+
104 | ... | ... | ... | ... | ... |
105 +----------------------+-------------------+-----------------+-------------------+----------------------+
106 </token>
107
108 <token name="@COMPUTE_CLUSTERS_HELP@">
109 recetox-aplcms - compute clusters
110 =================================
111
112 Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points.
113 Custom tolerances for `mz` and `rt` are computed based on the given parameters.
114 The tool takes a collection of all detected features and computes the clusters over a global feature table, adding the `sample_id` and `cluster` columns to the table.
115
116 Example Output
117 --------------
118
119 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
120 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
121 +======================+===================+=================+===================+======================+=====================+===============+
122 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
123 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
124 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
125 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
126 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
127 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
128 | ... | ... | ... | ... | ... | ... | ... |
129 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
130 </token>
131
132 <token name="@CORRECT_TIME_HELP@">
133 recetox-aplcms - correct time
134 =============================
135
136 Apply spline-based retention time correction to a feature table given the template table and the computed `mz` and `rt` tolerances.
137
138 Example Output
139 --------------
140 The output has the same format as `compute clusters` but the retention time values are corrected based on the template table.
141
142 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
143 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
144 +======================+===================+=================+===================+======================+=====================+===============+
145 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
146 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
147 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
148 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
149 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
150 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
151 | ... | ... | ... | ... | ... | ... | ... |
152 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
153 </token>
154 <token name="@COMPUTE_TEMPLATE_HELP@">
155 recetox-aplcms - compute template
156 =================================
157 Compute the template from a set of feature tables, choosing the one with the most features as the template.
158 </token>
159
160 <token name="@RECOVER_WEAKER_SIGNALS_HELP@">
161 recetox-aplcms - recover weaker signals
162 =======================================
163 Second stage peak detection based on the aligned feature table from the `feature alignment` step.
164 If a feature is contained in the aligned feature table, this step revisits the raw data and searches
165 for this feature at the retention time obtained by mapping the corrected retention time back to the original sample.
166
167 This recovers features which are present in a sample but might have been filtered out initially as noise due to low signal intensity.
168
169 Example Output
170 --------------
171 The table has the same format as the `compute clusters` output but might contain additional features which have been extracted based
172 on their presence in the aligned feature table.
173
174 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
175 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
176 +======================+===================+=================+===================+======================+=====================+===============+
177 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
178 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
179 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
180 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
181 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
182 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
183 | ... | ... | ... | ... | ... | ... | ... |
184 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
185 </token>
186
187 <token name="@ALIGN_FEATURES_HELP@">
188 recetox-aplcms - align features
189 ===============================
190 This step performs feature alignment after clustering and retention time correction.
191 The peaks clustered across samples are grouped based on the given tolerances to create an aligned feature table, connecting identical features across samples.
192 The parameter controls in how many samples a feature has to be detected at least in order to be included in the aligned feature table.
193
194 Example Output
195 --------------
196 The tool outputs 3 tables: the peak related `metadata`, the `retention times` and the `intensities` for all features across all samples.
197
198 Metadata Table
199 ~~~~~~~~~~~~~~
200 The `npeaks` column denotes the number of peaks which have been grouped into this feature. The columns with the sample names indicate whether this feature is present in the sample.
201
202 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
203 | id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
204 +=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
205 | 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 |
206 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
207 | 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 |
208 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
209 | 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 |
210 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
211 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
212 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
213
214 Intensity Table
215 ~~~~~~~~~~~~~~~
216 This table contains the peak area for aligned features in all samples.
217
218 +-------+------------------------+------------------------+------------------------+
219 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
220 +=======+========================+========================+========================+
221 | 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 |
222 +-------+------------------------+------------------------+------------------------+
223 | 2 | 2075168.6398983458 | 0 | 2574362.159289044 |
224 +-------+------------------------+------------------------+------------------------+
225 | 57 | 2934524.4406785755 | 1333044.5065971944 | 0 |
226 +-------+------------------------+------------------------+------------------------+
227 | ... | ... | ... | ... |
228 +-------+------------------------+------------------------+------------------------+
229
230 Retention Time Table
231 ~~~~~~~~~~~~~~~~~~~~
232 This table contains the retention times for all aligned features in all samples.
233
234 +-------+------------------------+------------------------+------------------------+
235 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
236 +=======+========================+========================+========================+
237 | 1 | 294.09792478513236 | 294.1499853056912 | 294.0634942428341 |
238 +-------+------------------------+------------------------+------------------------+
239 | 2 | 140.57625284242982 | 0 | 143.33575827589172 |
240 +-------+------------------------+------------------------+------------------------+
241 | 57 | 294.07200187644435 | 293.9406777222317 | 0 |
242 +-------+------------------------+------------------------+------------------------+
243 | ... | ... | ... | ... |
244 +-------+------------------------+------------------------+------------------------+
245 </token>
246
247 <token name="@MERGE_KNOWN_TABLES_HELP@">
248 recetox-aplcms - merge known table
249 ==================================
250
251 This tool allows merging the detected features back into the table of known features and vice versa.
252 It is used in the hybrid version of recetox-aplcms to augment the aligned feature table with the suspect peaks
253 and to augment this table with successfully detected features.
254 </token>
255 </macros>