Mercurial > repos > recetox > matchms_metadata_export
comparison matchms_metadata_export.xml @ 0:dfdbccfa8753 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit c10d901c526d0895869d18a1d1bdd1ea58ed7473
author | recetox |
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date | Thu, 18 May 2023 14:07:28 +0000 |
parents | |
children | f04610d25411 |
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-1:000000000000 | 0:dfdbccfa8753 |
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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> |