Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

comparison macros.xml @ 0:e2e2e455fcfb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c60206d37ba8fef418ba2a2bfcb4d3b8a70ab8c3"
author recetox
date Fri, 29 Oct 2021 09:49:13 +0000
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children 8fcf5ca25f5d
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-1:000000000000 0:e2e2e455fcfb
1 <macros>
2 <token name="@TOOL_VERSION@">0.9.0</token>
3 <xml name="requirements">
4 <requirements>
5 <container type="docker">recetox/recetox-xmsannotator:october4</container>
6 </requirements>
7 </xml>
8 <xml name="creator">
9 <creator>
10 <organization
11 url="https://www.recetox.muni.cz/"
12 name="RECETOX MUNI" />
13 </creator>
14 </xml>
15 <xml name="inputs">
16 <param name="peak_table" type="data" format="csv,parquet">
17 <label>Peak table</label>
18 <help><![CDATA[
19 A peak-intensity table such as outputted from apLCMS.
20 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
21 Columns for feature intensity in a sample have to start with <em>intensity</em>.
22
23 ]]></help>
24 </param>
25 <param name="compound_table" type="data" format="csv,parquet">
26 <label>Compound database</label>
27 <help><![CDATA[
28 Database of compounds according to which the annotation is performed.
29 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
30 ]]></help>
31 </param>
32 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
33 <label>Adduct database (optional)</label>
34 <help><![CDATA[
35 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
36 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
37 ]]></help>
38 </param>
39 </xml>
40
41 <xml name="outputs">
42 <data name="annotation_parquet" format="parquet"/>
43 </xml>
44
45 <xml name="tolerance">
46 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
47 <label>Mass tolerance [ppm]</label>
48 <help>Mass tolerance in ppm for database matching.</help>
49 </param>
50 <yield/>
51 </xml>
52 <token name="@HELP@">
53 <![CDATA[
54 Annotate the peak intensity table (e.g. from an apLCMS run) with compounds from the compounds database
55 using advanced methods.
56
57 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
58 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
59 withing some tolerance.
60 ]]>
61 </token>
62 <xml name="citations">
63 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
64 </xml>
65 </macros>