annotate macros.xml @ 1:e8962c8340f4 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
author recetox
date Mon, 03 Apr 2023 14:57:14 +0000
parents 2810c956ec39
children 73d8537dcbd6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
1 <macros>
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">0.10.3</token>
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
3 <xml name="requirements">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
4 <requirements>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">r-recetox-aplcms</requirement>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
6 <requirement type="package" version="2.5.2">pymzml</requirement>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
7 </requirements>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
8 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
9
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
10 <xml name="creator">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
11 <creator>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
12 <person
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
13 givenName="Maksym"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
14 familyName="Skoryk"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
15 url="https://github.com/maximskorik"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
16 identifier="0000-0003-2056-8018" />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
17 <person
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
18 givenName="Matej"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
19 familyName="Troják"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
20 url="https://github.com/xtrojak"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
21 identifier="0000-0003-0841-2707" />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
22 <person
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
23 givenName="Martin"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
24 familyName="Čech"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
25 url="https://github.com/martenson"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
26 identifier="0000-0002-9318-1781" />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
27 <person
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
28 givenName="Jiří"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
29 familyName="Novotný"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
30 url="https://github.com/xtracko"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
31 identifier="0000-0001-5449-3523" />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
32 <person
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
33 givenName="Helge"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
34 familyName="Hecht"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
35 url="https://github.com/hechth"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
36 identifier="0000-0001-6744-996X" />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
37 <organization
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
38 url="https://www.recetox.muni.cz/"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
39 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
40 name="RECETOX MUNI"/>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
41 </creator>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
42 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
43
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
44 <xml name="remove_noise_params">
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
45 <param name="min_pres" type="float" value="0.5" label="Minimal signal presence [fraction of scans]"
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
46 help="The minimum proportion of presence in the time period for a series of signals grouped by m/z to be considered a peak." />
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
47 <param name="min_run" type="float" value="12" label="Minimal elution time [unit corresponds to the retention time]"
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
48 help="The minimum length of elution time for a series of signals grouped by m/z to be considered a peak." />
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
49 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
50 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
51 This value, multiplied by the m/z value, becomes the cutoff level.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
52 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
53 <param name="baseline_correct" type="float" value="0" label="Baseline correction [unit of signal intensity]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
54 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." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
55 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Weight intensity"
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
56 help="Whether to weight the local density by signal intensities in initial peak detection." />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
57 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
58
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
59 <xml name="generate_feature_table_params">
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
60 <param name="BIC_factor" type="float" value="2.0" label="BIC factor"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
61 help="A factor influencing Bayesian information criterion (BIC) in estimation of RT peak shape.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
62 If the value is larger than 1, models with more peaks are penalized more." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
63 <section name="advanced" title="Advanced" expanded="false">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
64 <param name="component_eliminate" type="float" value="0.01" label="Component eliminate"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
65 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." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
66 <section name="shape_model" title="Shape model deviations" expanded="true">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
67 <param name="sigma_ratio_lim_min" type="float" optional="true" label="Minimal sigma ratio"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
68 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." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
69 <param name="sigma_ratio_lim_max" type="float" optional="true" label="Maximal sigma ratio"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
70 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." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
71 </section>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
72 <conditional name="sd_cut">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
73 <param name="sd_cut_bounds" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Standard deviations boundaries."
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
74 help="Do not apply any limitations on the standard deviations." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
75 <when value="FALSE">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
76 <param name="sd_cut_min" type="float" value="0.01" label="Minimal standard deviation"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
77 help="The minimum standard deviation - features with a standard deviation lower than this number are eliminated." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
78 <param name="sd_cut_max" type="float" value="500" label="Maximal standard deviation"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
79 help="The maximum standard deviation - features with a standard deviation greater than this number are eliminated." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
80 </when>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
81 </conditional>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
82 <conditional name="peak_estim">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
83 <param name="peak_estim_method" type="select" display="radio" label="Peak estimation method"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
84 help="The estimation method for parameters of the bi-Gaussian peak model. Two possible algorithms: moment and EM (expectation maximization).">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
85 <option value="moment">Moment</option>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
86 <option value="EM" selected="true">EM</option>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
87 </param>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
88 <when value="moment">
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
89 <param name="moment_power" type="float" value="1" label="Moment power"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
90 help="The power parameter for data transformation when fitting the bi-Gaussian mixture model in an EIC." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
91 </when>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
92 </conditional>
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
93 </section>
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
94 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
95
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
96 <xml name="compute_clusters_params">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
97 <conditional name="tolerances_input_method">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
98 <param name="input_method" type="select" display="radio" label="Tolerances input method"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
99 help="Tolerances can be entered directly or loaded from a file.">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
100 <option value="direct" selected="true">direct</option>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
101 <option value="file">file</option>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
102 </param>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
103 <when value="direct">
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
104 <param name="mz_tol_relative" type="float" optional="true" label="Relative m/z tolerance"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
105 help="Relative m/z tolerance to use for grouping features.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
106 If not provided, it is calculated from the data using kernel density estimation." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
107 <param name="rt_tol_relative" type="float" optional="true" label="Relative rt tolerance [unit corresponds to the retention time]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
108 help="Relative retention time tolerance to use for grouping features.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
109 If not provided, it is calculated from the data using kernel density estimation." />
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
110 </when>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
111 <when value="file">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
112 <param label="Input tolerances values" name="input_tolerances" type="data" format="parquet"
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
113 help="Table containing tolerance values." />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
114 </when>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
115 </conditional>
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
116 <param name="mz_tol_absolute" type="float" label="Minimal absolute m/z tolerance [Da]" value="1e-05"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
117 help="During the clustering, an m/z tolerance is computed based on the data and the specified relative tolerance.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
118 This parameter allows the specification of a minimal value of this tolerance." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
119 <param name="mz_max_diff" type="float" label="Maximal m/z difference [Da]" value="0.01"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
120 help="Maximum allowed difference between feature m/z values to belong to the same cluster." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
121
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
122 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
123
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
124 <xml name="recover_weaker_params">
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
125 <param name="mz_tol" type="float" value="10" label="m/z tolerance [ppm]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
126 help="The m/z tolerance level for the grouping of data points. This value is expressed as the fraction of the m/z value.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
127 This value, multiplied by the m/z value, becomes the cutoff level.
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
128 The recommended value is the machine's nominal accuracy level (e.g. for FTMS, it is 10)." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
129 <param name="recover_mz_range" type="float" optional="true" label="Range for m/z recovery [ppm]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
130
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
131 help="The m/z around the feature m/z to search for observations. If not given, 1.5 times the m/z tolerance
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
132 in the aligned object will be used." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
133 <param name="recover_rt_range" type="float" optional="true" label="Range for rt recovery [unit of retention time]"
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
134 help="The retention time around the feature retention time to search for observations.
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
135 If not given, 0.5 times the retention time tolerance in the aligned object will be used." />
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
136 <param name="use_observed_range" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
137 label="Use observed rt range" help="Use the minimal and maximal rt values per feature." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
138 <param name="recover_min_count" type="integer" value="3" label="Minimal count to recover"
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
139 help="The minimum number of raw data points to be considered as a true feature." />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
140 <param name="intensity_weighted" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE"
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
141 label="Weight intensity" help="Whether to weight the local density by signal intensities in initial peak detection." />
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
142 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
143
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
144 <xml name="bandwidth_params">
1
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
145 <param name="bandwidth" type="float" value="0.5" label="Bandwidth factor" min="0" max="1"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
146 help="Parameter used to scale down the overall range of retention times (the bandwidth) assumed in the kernel smoother
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
147 used for peak identification. The value is between zero and one. The minimal and maximal bandwidth can be limited by explicit values." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
148 <param name="min_bandwidth" type="float" optional="true" label="Minimal bandwidth [unit corresponds to the retention time]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
149 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." />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
150 <param name="max_bandwidth" type="float" optional="true" label="Maximal bandwidth [unit corresponds to the retention time]"
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
151 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" />
e8962c8340f4 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
recetox
parents: 0
diff changeset
152
0
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
153 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
154
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
155 <xml name="citations">
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
156 <citations>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
157 <citation type="doi">10.1093/bioinformatics/btp291</citation>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
158 <citation type="doi">10.1186/1471-2105-11-559</citation>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
159 <citation type="doi">10.1021/pr301053d</citation>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
160 <citation type="doi">10.1093/bioinformatics/btu430</citation>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
161 <citation type="doi">10.1038/s41598-020-70850-0</citation>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
162 <yield />
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
163 </citations>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
164 </xml>
2810c956ec39 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
recetox
parents:
diff changeset
165 </macros>