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comparison matchms_metadata_export.xml @ 0:dfdbccfa8753 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c10d901c526d0895869d18a1d1bdd1ea58ed7473
author recetox
date Thu, 18 May 2023 14:07:28 +0000
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1 <tool id="matchms_metadata_export" name="matchms metadata export " version="0.19.0+galaxy0" profile="21.05">
2 <description>extract all metadata from mass spectra file to tabular format</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator"/>
7 <requirements>
8 <requirement type="package" version="0.19.0">matchms</requirement>
9 </requirements>
10
11 <command detect_errors='aggressive'><![CDATA[
12 python ${matchms_python_cli}
13 ]]></command>
14
15 <configfiles>
16 <configfile name="matchms_python_cli">
17 import pandas
18 from matchms.importing import load_from_msp, load_from_mgf
19 from matchms.exporting.metadata_export import export_metadata_as_csv
20
21 spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))
22
23 export_metadata_as_csv(spectra_list, "${output_file}")
24 </configfile>
25 </configfiles>
26
27 <inputs>
28 <param label="Spectra file" name="input_file" type="data" format="msp,mgf" help="Mass spectral library file."/>
29 <param label="Harmonize metadata" name="harmonize_metadata" type="boolean" truevalue="True" falsevalue="False"
30 checked="false" help="Apply harmonization process on the metadata keys (e.g. parse numeric values, derive precursor mass)."/>
31 </inputs>
32
33 <outputs>
34 <data label="matchms extract metadata on ${on_string}" name="output_file" format="csv"/>
35 </outputs>
36
37 <tests>
38 <test>
39 <param name="input_file" value="convert/mgf_out.mgf" ftype="mgf"/>
40 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
41 </test>
42 <test>
43 <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
44 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
45 </test>
46 </tests>
47
48 <help><![CDATA[
49 Documentation
50 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
51 This tool can be used to export the metadata accompanying the actual spectral information to a tabular file.
52
53 During harmonization of metadata, some of the keywords might change during the conversion process to a unified form.
54
55 For more documentation on the matchms library see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.
56 ]]></help>
57
58 <expand macro="citations"/>
59 </tool>