Mercurial > repos > recetox > recetox_xmsannotator_advanced

comparison macros.xml @ 5:a393c4383436 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
author recetox
date Mon, 26 Jun 2023 13:55:44 +0000
parents 464c1e80a01f
children
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4:464c1e80a01f 5:a393c4383436
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.9.0</token> 2 <token name="@TOOL_VERSION@">0.10.0</token>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.9.0">r-recetox-xmsannotator</requirement>
6 </requirements>
7 </xml>
8 <xml name="creator">
9 <creator>
10 <person
11 givenName="Jiří"
12 familyName="Novotný"
13 url="https://github.com/xtracko"
14 identifier="0000-0001-5449-3523" />
15 <person
16 givenName="Martin"
17 familyName="Čech"
18 url="https://github.com/martenson"
19 identifier="0000-0002-9318-1781" />
20 <organization
21 url="https://www.recetox.muni.cz/"
22 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
23 name="RECETOX MUNI" />
24 </creator>
25 </xml>
26 <xml name="inputs">
27 <param name="peak_table" type="data" format="csv,h5,parquet">
28 <label>Peak table</label>
29 <help><![CDATA[
30 A peak-intensity table such as outputted from apLCMS.
31 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
32 ]]></help>
33 </param>
34 <param name="compound_table" type="data" format="csv,parquet">
35 <label>Compound database</label>
36 <help><![CDATA[
37 Database of compounds according to which the annotation is performed.
38 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
39 ]]></help>
40 </param>
41 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
42 <label>Adduct database (optional)</label>
43 <help><![CDATA[
44 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
45 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
46 ]]></help>
47 </param>
48 </xml>
49 3
50 <xml name="outputs"> 4 <xml name="requirements">
51 <data name="annotation_parquet" format="parquet"/> 5 <requirements>
52 </xml> 6 <requirement type="package" version="@TOOL_VERSION@">r-recetox-xmsannotator</requirement>
7 </requirements>
8 </xml>
53 9
54 <xml name="tolerance"> 10 <xml name="creator">
55 <param name="mass_tolerance_ppm" type="integer" min="0" value="5"> 11 <creator>
56 <label>Mass tolerance [ppm]</label> 12 <person
57 <help>Mass tolerance in ppm for database matching.</help> 13 givenName="Jiří"
58 </param> 14 familyName="Novotný"
59 <yield/> 15 url="https://github.com/xtracko"
60 </xml> 16 identifier="0000-0001-5449-3523" />
61 <token name="@HELP@"> 17 <person
62 <![CDATA[ 18 givenName="Martin"
63 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database 19 familyName="Čech"
64 using advanced methods. 20 url="https://github.com/martenson"
21 identifier="0000-0002-9318-1781" />
22 <person
23 givenName="Matej"
24 familyName="Troják"
25 url="https://github.com/xtrojak"
26 identifier="0000-0003-0841-2707" />
27 <organization
28 url="https://www.recetox.muni.cz/"
29 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
30 name="RECETOX MUNI" />
31 </creator>
32 </xml>
65 33
66 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured 34 <xml name="inputs">
67 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are 35 <param name="metadata_table" type="data" format="parquet,csv">
68 withing some tolerance. 36 <label>Metadata table</label>
69 ]]> 37 <help><![CDATA[
70 </token> 38 Peak metadata table*.
71 <xml name="citations"> 39 ]]></help>
72 <citation type="doi">10.1021/acs.analchem.6b01214</citation> 40 </param>
73 </xml> 41 <param name="intensity_table" type="data" format="parquet,csv">
42 <label>Intensity table</label>
43 <help><![CDATA[
44 Table with intensities** for features (rows) across samples (columns).
45 ]]></help>
46 </param>
47 <param name="compound_table" type="data" format="parquet,csv">
48 <label>Compound database</label>
49 <help><![CDATA[
50 Database of compounds according to which the annotation is performed.
51 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
52 ]]></help>
53 </param>
54 <param name="adduct_table" type="data" format="parquet,csv" optional="true">
55 <label>Adduct database</label>
56 <help><![CDATA[
57 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
58 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
59 ]]></help>
60 </param>
61 <param name="adduct_weights" type="data" format="parquet,csv" optional="true">
62 <label>Adduct weights</label>
63 <help>
64 A weight-by-adduct table.
65 </help>
66 </param>
67 </xml>
68
69 <xml name="outputs">
70 <data name="output_file" format="parquet">
71 <change_format>
72 <when input="metadata_table.ext" value="csv" format="csv" />
73 </change_format>
74 </data>
75 </xml>
76
77 <xml name="tolerance">
78 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
79 <label>Mass tolerance [ppm]</label>
80 <help>Mass tolerance in ppm for database matching.</help>
81 </param>
82 <yield/>
83 </xml>
84
85 <token name="@HELP@">
86 Description
87 ===========
88
89 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
90 using advanced methods.
91
92 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
93 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
94 withing some tolerance.
95
96 Then, a score and a confidence level is assigned to each match based on peak correlation
97 clustering, metabolite pathway associations, adducts expectations, and isotope conformations.
98
99 Input tables description
100 ------------------------
101
102 (*) Metadata table
103 ~~~~~~~~~~~~~~~~~~
104
105 The output from recetox-aplcms tool.
106 The `npeaks` column denotes the number of peaks which have been grouped into this feature.
107 The columns with the sample names indicate whether this feature is present in the sample.
108 Only id, mz, and rt columns are required to be present.
109
110 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
111 | id | mz | mzmin | mzmax | rt | rtmin | rtmax | npeaks | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
112 +=======+==============+==============+===============+================+===============+===============+===========+========================+========================+========================+
113 | 1 | 70.03707021 | 70.037066 | 70.0370750 | 294.1038014 | 294.0634942 | 294.149985 | 3 | 1 | 1 | 1 |
114 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
115 | 2 | 70.06505677 | 70.065045 | 70.0650676 | 141.9560055 | 140.5762528 | 143.335758 | 2 | 1 | 0 | 1 |
116 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
117 | 57 | 78.04643252 | 78.046429 | 78.0464325 | 294.0063397 | 293.9406777 | 294.072001 | 2 | 1 | 1 | 0 |
118 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
119 | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
120 +-------+--------------+--------------+---------------+----------------+---------------+---------------+-----------+------------------------+------------------------+------------------------+
121
122 (**) Intensity table
123 ~~~~~~~~~~~~~~~~~~~~
124
125 The output from recetox-aplcms tool.
126 This table contains the peak area for aligned features in all samples.
127
128 +-------+------------------------+------------------------+------------------------+
129 | id | 21_qc_no_dil_milliq | 29_qc_no_dil_milliq | 8_qc_no_dil_milliq |
130 +=======+========================+========================+========================+
131 | 1 | 13187487.20482895 | 7957395.699119729 | 11700594.397257797 |
132 +-------+------------------------+------------------------+------------------------+
133 | 2 | 2075168.6398983458 | 0 | 2574362.159289044 |
134 +-------+------------------------+------------------------+------------------------+
135 | 57 | 2934524.4406785755 | 1333044.5065971944 | 0 |
136 +-------+------------------------+------------------------+------------------------+
137 | ... | ... | ... | ... |
138 +-------+------------------------+------------------------+------------------------+
139 </token>
140
141 <xml name="citations">
142 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
143 </xml>
74 </macros> 144 </macros>