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comparison xmsannotator_macros.xml @ 5:47185b5abe9e draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
author recetox
date Mon, 14 Dec 2020 03:33:44 +0000
parents 3bdef6d114fd
children 53246490912c
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4:6b2b2b83b46c 5:47185b5abe9e
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.3.2</token> 2 <token name="@TOOL_VERSION@">1.3.2</token>
3 <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox0</token> 3 <token name="@DOCKER_IMAGE@">recetox/xmsannotator:1.3.2-recetox2</token>
4 4
5 <xml name="annotation"> 5 <xml name="inputs">
6 <param name="peaks" type="data" format="h5" label="Peaks" help="Peaks to annotate."/> 6 <param name="peak_table" type="data" format="csv,h5,parquet">
7 <param name="adducts" type="data" format="h5" label="Adduct database"/> 7 <label>Peak table</label>
8 <param name="compounds" type="data" format="h5" label="Compound database"/> 8 <help><![CDATA[
9 A peak-intensity table such as outputted from apLCMS.
10 The file is required to contain the fields <em>mz</em> and <em>rt</em>.
11 ]]></help>
12 </param>
13 <param name="compound_table" type="data" format="csv,parquet">
14 <label>Compound database</label>
15 <help><![CDATA[
16 Database of compounds according to which the annotation is performed.
17 The database is required to contain the fields <em>compound_id</em>, <em>monoisotopic_mass</em>, and <em>molecular_formula</em>.
18 ]]></help>
19 </param>
20 <param name="adduct_table" type="data" format="csv,parquet" optional="true">
21 <label>Adduct database (optional)</label>
22 <help><![CDATA[
23 Database of adduct which is combined with the database of compound to form a molecule-adduct pairs.
24 The database is required to contain <em>adduct</em>, <em>charge</em>, <em>mass</em>, and <em>n_molecules</em>.
25 ]]></help>
26 </param>
27 </xml>
9 28
10 <param name="mz_tolerance_ppm" type="float" value="5" min="0" label="Mass tolerance [ppm]" help="Mass tolerance in ppm for database matching."/> 29 <xml name="outputs">
30 <data name="annotation_parquet" format="parquet"/>
31 </xml>
32
33 <xml name="tolerance">
34 <param name="mass_tolerance_ppm" type="integer" min="0" value="5">
35 <label>Mass tolerance [ppm]</label>
36 <help>Mass tolerance in ppm for database matching.</help>
37 </param>
38 <yield/>
11 </xml> 39 </xml>
12 40
13 <xml name="citations"> 41 <xml name="citations">
14 <citations> 42 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
15 <citation type="doi">10.1021/acs.analchem.6b01214</citation>
16 </citations>
17 </xml> 43 </xml>
18 </macros> 44 </macros>