Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate macros.xml @ 7:c3d4b82c7e5d draft

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 199dd33897bacaeb194ce9f5239cc4752c92e4df
author recetox
date Thu, 22 Jun 2023 11:46:55 +0000
parents 755ff0afaaff
children 99d118321d5f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
1 <macros>
4
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
2 <token name="@TOOL_VERSION@">0.11.0</token>
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
3 <xml name="requirements">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
4 <requirements>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
6 <requirement type="package" version="2.5.2">pymzml</requirement>
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
7 </requirements>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
8 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
9
7
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
10 <xml name="annotation">
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
11 <edam_topics>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
12 <edam_topic>topic_3172</edam_topic>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
13 <edam_topic>topic_0091</edam_topic>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
14 <edam_topic>topic_3520</edam_topic>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
15 </edam_topics>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
16 <xrefs>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
17 <xref type="bio.tools">recetox-aplcms</xref>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
18 </xrefs>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
19 </xml>
c3d4b82c7e5d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
recetox
parents: 4
diff changeset
20
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
21 <xml name="creator">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
22 <creator>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
23 <person
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
24 givenName="Maksym"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
25 familyName="Skoryk"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
26 url="https://github.com/maximskorik"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
27 identifier="0000-0003-2056-8018" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
28 <person
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
29 givenName="Matej"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
30 familyName="Troják"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
31 url="https://github.com/xtrojak"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
32 identifier="0000-0003-0841-2707" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
33 <person
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
34 givenName="Martin"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
35 familyName="Čech"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
36 url="https://github.com/martenson"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
37 identifier="0000-0002-9318-1781" />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
38 <person
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
39 givenName="Jiří"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
40 familyName="Novotný"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
41 url="https://github.com/xtracko"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
42 identifier="0000-0001-5449-3523" />
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
43 <person
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
44 givenName="Helge"
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
45 familyName="Hecht"
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
46 url="https://github.com/hechth"
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
47 identifier="0000-0001-6744-996X" />
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
48 <organization
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
49 url="https://www.recetox.muni.cz/"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
50 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
51 name="RECETOX MUNI"/>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
52 </creator>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
53 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
54
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
55 <xml name="remove_noise_params">
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
56 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]"
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
57 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
58 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
59 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
60 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
61 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
62 This value, multiplied by the m/z value, becomes the cutoff level.
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
63 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
64 <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
65 help="After grouping the observations, the highest intensity in each group is found. If the highest is lower than this value, the entire group will be deleted." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
66 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity"
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
67 help="Whether to weight the local density by signal intensities in initial peak detection." />
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
68 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
69
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
70 <xml name="generate_feature_table_params">
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
71 <param name="BIC_factor" type="float" value="2.0" label="BIC factor"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
72 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape.
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
73 If the value is larger than 1, models with more peaks are penalized more." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
74 <section name="advanced" title="Advanced" expanded="false">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
75 <param name="component_eliminate" type="float" value="0.01" label="Component eliminate"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
76 help="In fitting mixture of bi-Gaussian model of an EIC, when a component accounts for a proportion of intensities less than this value, the component will be ignored." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
77 <section name="shape_model" title="Shape model deviations" expanded="true">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
78 <param name="sigma_ratio_lim_min" type="float" optional="true" label="Minimal sigma ratio"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
79 help="The lower limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
80 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
81 help="The upper limit of the ratio range between the left-standard deviation and the right-standard deviation of the bi-Gaussian function to fit the data." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
82 </section>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
83 <conditional name="sd_cut">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
84 <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
85 help="Do not apply any limitations on the standard deviations." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
86 <when value="FALSE">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
87 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
88 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
89 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
90 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
91 </when>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
92 </conditional>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
93 <conditional name="peak_estim">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
94 <param name="peak_estim_method" type="select" display="radio" label="Peak estimation method"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
95 help="The estimation method for parameters of the bi-Gaussian peak model. Two possible algorithms: moment and EM (expectation maximization).">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
96 <option value="moment">Moment</option>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
97 <option value="EM" selected="true">EM</option>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
98 </param>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
99 <when value="moment">
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
100 <param name="moment_power" type="float" value="1" label="Moment power"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
101 help="The power parameter for data transformation when fitting the bi-Gaussian mixture model in an EIC." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
102 </when>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
103 </conditional>
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
104 </section>
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
105 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
106
4
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
107 <xml name="tolerances">
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
108 <param name="mz_tol_relative_ppm" type="float" value="10" label="Relative m/z tolerance [ppm]"
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
109 help="Relative m/z tolerance to use for grouping features." />
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
110 <param name="rt_tol" type="float" value="5" label="Retention time tolerance [unit corresponds to the retention time]"
755ff0afaaff planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
recetox
parents: 3
diff changeset
111 help="Retention time tolerance to use for grouping features." />
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
112 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
113
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
114 <xml name="recover_weaker_params">
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
115 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
116 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
117 This value, multiplied by the m/z value, becomes the cutoff level.
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
118 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
119 <param name="recover_mz_range" type="float" optional="true" label="Range for m/z recovery [ppm]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
120
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
121 help="The m/z around the feature m/z to search for observations. If not given, 1.5 times the m/z tolerance
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
122 in the aligned object will be used." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
123 <param name="recover_rt_range" type="float" optional="true" label="Range for rt recovery [unit of retention time]"
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
124 help="The retention time around the feature retention time to search for observations.
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
125 If not given, 0.5 times the retention time tolerance in the aligned object will be used." />
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
126 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
127 label="Use observed rt range" help="Use the minimal and maximal rt values per feature." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
128 <param name="recover_min_count" type="integer" value="3" label="Minimal count to recover"
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
129 help="The minimum number of raw data points to be considered as a true feature." />
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
130 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
131 label="Weight intensity" help="Whether to weight the local density by signal intensities in initial peak detection." />
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
132 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
133
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
134 <xml name="bandwidth_params">
3
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
135 <param name="bandwidth" type="float" value="0.5" label="Bandwidth factor" min="0" max="1"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
136 help="Parameter used to scale down the overall range of retention times (the bandwidth) assumed in the kernel smoother
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
137 used for peak identification. The value is between zero and one. The minimal and maximal bandwidth can be limited by explicit values." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
138 <param name="min_bandwidth" type="float" optional="true" label="Minimal bandwidth [unit corresponds to the retention time]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
139 help="The lower limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile." />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
140 <param name="max_bandwidth" type="float" optional="true" label="Maximal bandwidth [unit corresponds to the retention time]"
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
141 help="The upper limit on the resulting bandwidth. If not given, it is estimated based on the overall range of retention times in the profile" />
c69a12bfc2fb planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 2
diff changeset
142
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
143 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
144
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
145 <xml name="citations">
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
146 <citations>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
147 <citation type="doi">10.1093/bioinformatics/btp291</citation>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
148 <citation type="doi">10.1186/1471-2105-11-559</citation>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
149 <citation type="doi">10.1021/pr301053d</citation>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
150 <citation type="doi">10.1093/bioinformatics/btu430</citation>
2
472dc85ce7c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents: 0
diff changeset
151 <citation type="doi">10.1038/s41598-020-70850-0</citation>
0
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
152 <yield />
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
153 </citations>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
154 </xml>
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
recetox
parents:
diff changeset
155 </macros>