Mercurial > repos > recetox > recetox_aplcms_compute_template

annotate help.xml @ 6:9c9accecae6e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 0873c036d734782d2647b0eea84cd1a0658f5e58
author recetox
date Wed, 19 Jul 2023 00:23:43 +0000
parents 933e9aad0e4a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
1 <macros>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
2
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
3 <token name="@GENERAL_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
4 General Information
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
5 ===================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
6
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
7 Overview
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
8 --------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
9
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
10 recetox-aplcms is a software package for peak detection in high resolution mass spectrometry (HRMS) data.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
11 It supports reading .mzml files in raw profile mode and uses a bi-Gaussian chromatographic peak shape for feature detection and quantification.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
12
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
13 recetox-aplcms is based on the apLCMS package developed by Tianwei Yu at Emory University - see the citations and the apLCMS section beneath.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
14 This version includes various software updates and is actively developed and maintained on `GitHub`_.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
15 Please submit eventual bug reports as `issues`_ on the repository.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
16
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
17 .. _GitHub: https://github.com/RECETOX/recetox-aplcms
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
18 .. _issues: https://github.com/RECETOX/recetox-aplcms/issues/new
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
19
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
20
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
21 Workflow
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
22 --------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
23
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
24 .. image:: https://raw.githubusercontent.com/RECETOX/galaxytools/aee0dd6cf6c05936269efe4337c50e27cc68e86b/tools/recetox_aplcms/images/scheme.png
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
25 :width: 2560
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
26 :height: 788
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
27 :scale: 40
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
28 :alt: A picture of a workflow diagram.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
29
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
31 The workflows consist of the following building blocks:
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
32
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
33 (1) remove noise - denoise the raw data and extract the EIC
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
34 (2) generate feature table - group features in EIC into peaks using peak-shape model
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
35 (3) compute clusters - compute mz and rt clusters across samples
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
36 (4) compute template - find the template for rt correction
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
37 (5) correct time - correct the rt across samples using splines
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
38 (6) align features - align identical features across samples
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
39 (7) recover weaker signals - recover missed features in samples based on the aligned features
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
40 (8) merge known table - add known features to detected features table and vice versa
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
41
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
42 For detailed documentation on the individual steps please see the individual tool wrappers.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
43
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
44
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
45 apLCMS (Original Reference)
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
46 ---------------------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
47
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
48 apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
49 tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
50 Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
51 correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
52 please refer to https://mypage.cuhk.edu.cn/academics/yutianwei/apLCMS/.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
53 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
54
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
55 <token name="@REMOVE_NOISE_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
56 recetox-aplcms - remove noise
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
57 =============================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
58
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
59 This tool is the first step of recetox-aplcms.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
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).
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
61 Only peaks with a minimum elution length of `min_run` seconds are kept.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
62
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
63 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
64 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
66 See an example output in the table below. The `group_number` column indicates the cluster index.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
67
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
68 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
69 | mz | rt | intensity | group_number |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
70 +======================+===================+=======================+====================+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
71 | 70.01060119055192 | 350.58654 | 21178.330810546875 | 5 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
72 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
73 | 70.02334120404554 | 130.175262 | 287869.5478515625 | 10 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
74 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
75 | 70.0287408273165 | 134.801352 | 60883.15185546875 | 11 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
76 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
77 | 70.02872416715464 | 183.991896 | 9201.574584960938 | 11 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
78 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
79 | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
80 +----------------------+-------------------+-----------------------+--------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
81 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
82
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
83 <token name="@GENERATE_FEATURE_TABLE_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
84 recetox-aplcms - generate feature table
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
85 =======================================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
86 The second step in the recetox-aplcms workflow performing peak shape parameter estimation.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
87
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
89
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
90
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
91 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
92 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
94
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
95 +----------------------+-------------------+-----------------+-------------------+----------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
96 | mz | rt | sd1 | sd2 | area |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
97 +======================+===================+=================+===================+======================+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
98 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.24595184 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
99 +----------------------+-------------------+-----------------+-------------------+----------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
100 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
101 +----------------------+-------------------+-----------------+-------------------+----------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
102 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.50659719 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
103 +----------------------+-------------------+-----------------+-------------------+----------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
104 | ... | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
105 +----------------------+-------------------+-----------------+-------------------+----------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
106 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
107
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
108 <token name="@COMPUTE_CLUSTERS_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
109 recetox-aplcms - compute clusters
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
110 =================================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
111
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
112 Group features with `mz` and `rt` using tolerances within the tolerance into clusters, creating larger features from raw data points.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
113 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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
114
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
115 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
116 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
117
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
118 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
119 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
120 +======================+===================+=================+===================+======================+=====================+===============+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
121 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
122 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
123 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
124 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
125 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
126 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
127 | ... | ... | ... | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
128 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
129 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
130
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
131 <token name="@CORRECT_TIME_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
132 recetox-aplcms - correct time
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
133 =============================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
134
2
933e9aad0e4a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 0
diff changeset
135 Apply spline-based retention time correction to a feature table given the template table and the `mz` and `rt` tolerances.
0
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
136
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
137 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
138 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
139 The output has the same format as `compute clusters` but the retention time values are corrected based on the template table.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
140
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
141 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
142 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
143 +======================+===================+=================+===================+======================+=====================+===============+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
144 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
145 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
146 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
147 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
148 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
149 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
150 | ... | ... | ... | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
151 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
152 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
153 <token name="@COMPUTE_TEMPLATE_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
154 recetox-aplcms - compute template
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
155 =================================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
156 Compute the template from a set of feature tables, choosing the one with the most features as the template.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
157 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
158
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
159 <token name="@RECOVER_WEAKER_SIGNALS_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
160 recetox-aplcms - recover weaker signals
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
161 =======================================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
162 Second stage peak detection based on the aligned feature table from the `feature alignment` step.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
163 If a feature is contained in the aligned feature table, this step revisits the raw data and searches
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
164 for this feature at the retention time obtained by mapping the corrected retention time back to the original sample.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
165
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
166 This recovers features which are present in a sample but might have been filtered out initially as noise due to low signal intensity.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
167
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
168 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
169 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
170 The table has the same format as the `compute clusters` output but might contain additional features which have been extracted based
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
171 on their presence in the aligned feature table.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
172
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
173 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
174 | mz | rt | sd1 | sd2 | area | sample_id | cluster |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
175 +======================+===================+=================+===================+======================+=====================+===============+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
176 | 70.02317542938793 | 142.36033 | 11.436659559 | 14.592754933 | 4159269.245951841 | 21_qc_no_dil_milliq | 7 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
177 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
178 | 70.02869594233522 | 205.48765 | 0.263230763 | 0.285101428707 | 8849767.11861127 | 21_qc_no_dil_milliq | 9 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
179 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
180 | 78.04643252598305 | 294.01713 | 0.51677558617 | 1.317028944141 | 1333044.506597194 | 21_qc_no_dil_milliq | 13 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
181 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
182 | ... | ... | ... | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
183 +----------------------+-------------------+-----------------+-------------------+----------------------+---------------------+---------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
184 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
185
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
186 <token name="@ALIGN_FEATURES_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
187 recetox-aplcms - align features
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
188 ===============================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
189 This step performs feature alignment after clustering and retention time correction.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
190 The peaks clustered across samples are grouped based on the given tolerances to create an aligned feature table, connecting identical features across samples.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
191 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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
192
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
193 Example Output
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
194 --------------
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
195 The tool outputs 3 tables: the peak related `metadata`, the `retention times` and the `intensities` for all features across all samples.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
196
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
197 Metadata Table
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
198 ~~~~~~~~~~~~~~
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
199 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.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
200
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
201 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
202 | id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
203 +=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
204 | 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
205 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
206 | 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
207 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
208 | 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
209 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
210 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
211 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
212
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
213 Intensity Table
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
214 ~~~~~~~~~~~~~~~
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
215 This table contains the peak area for aligned features in all samples.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
216
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
217 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
218 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
219 +=======+========================+========================+========================+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
220 | 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
221 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
222 | 2 | 2075168.6398983458 | 0 | 2574362.159289044 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
223 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
224 | 57 | 2934524.4406785755 | 1333044.5065971944 | 0 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
225 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
226 | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
227 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
228
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
229 Retention Time Table
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
230 ~~~~~~~~~~~~~~~~~~~~
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
231 This table contains the retention times for all aligned features in all samples.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
232
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
233 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
234 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
235 +=======+========================+========================+========================+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
236 | 1 | 294.09792478513236 | 294.1499853056912 | 294.0634942428341 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
237 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
238 | 2 | 140.57625284242982 | 0 | 143.33575827589172 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
239 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
240 | 57 | 294.07200187644435 | 293.9406777222317 | 0 |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
241 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
242 | ... | ... | ... | ... |
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
243 +-------+------------------------+------------------------+------------------------+
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
244 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
245
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
246 <token name="@MERGE_KNOWN_TABLES_HELP@">
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
247 recetox-aplcms - merge known table
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
248 ==================================
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
249
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
250 This tool allows merging the detected features back into the table of known features and vice versa.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
251 It is used in the hybrid version of recetox-aplcms to augment the aligned feature table with the suspect peaks
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
252 and to augment this table with successfully detected features.
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
253 </token>
1f22ec2823af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
254 </macros>