Mercurial > repos > recetox > matchms_convert
comparison matchms_convert.xml @ 0:f0ad1b8685fd draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
author | recetox |
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date | Tue, 02 May 2023 10:15:50 +0000 |
parents | |
children | 49ef4455b0c2 |
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-1:000000000000 | 0:f0ad1b8685fd |
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1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05"> | |
2 <description>convert between mass spectral library formats using matchms</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="creator"/> | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> | |
9 </requirements> | |
10 | |
11 <command detect_errors='aggressive'><![CDATA[ | |
12 python ${matchms_python_cli} | |
13 ]]></command> | |
14 | |
15 <configfiles> | |
16 <configfile name="matchms_python_cli"> | |
17 from matchms.importing import load_from_msp, load_from_mgf, load_from_json | |
18 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json | |
19 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", False)) | |
20 #if $output_format == "msp" | |
21 save_as_msp(spectra, "${converted_library}", write_peak_comments = False) | |
22 #else | |
23 save_as_${output_format}(spectra, "${converted_library}") | |
24 #end if | |
25 </configfile> | |
26 </configfiles> | |
27 | |
28 <inputs> | |
29 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json" help="Mass spectral library file to convert." /> | |
30 | |
31 <param label="Spectral library format" name="output_format" type="select" | |
32 help="Output format to convert the spectral library into."> | |
33 <option value="msp" selected="true">msp</option> | |
34 <option value="mgf">mgf</option> | |
35 <option value="json">json</option> | |
36 </param> | |
37 </inputs> | |
38 | |
39 <outputs> | |
40 <data label="${tool.name} from ${spectral_library.ext} to ${output_format} on ${on_string}" name="converted_library" format="msp"> | |
41 <change_format> | |
42 <when input="output_format" value="mgf" format="mgf" /> | |
43 <when input="output_format" value="json" format="json" /> | |
44 </change_format> | |
45 </data> | |
46 </outputs> | |
47 | |
48 <tests> | |
49 <test> | |
50 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/> | |
51 <param name="output_format" value="mgf"/> | |
52 <output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/> | |
53 </test> | |
54 <test> | |
55 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/> | |
56 <param name="output_format" value="json"/> | |
57 <output name="converted_library" file="convert/json_out.json" ftype="json"/> | |
58 </test> | |
59 <test> | |
60 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/> | |
61 <param name="output_format" value="msp"/> | |
62 <output name="converted_library" file="convert/msp_out.msp" ftype="msp"/> | |
63 </test> | |
64 </tests> | |
65 | |
66 | |
67 <help><![CDATA[ | |
68 Documentation | |
69 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`. | |
70 This tool can be used to convert from one library format to another. | |
71 | |
72 Please note that peak comments in `RIKEN` style `msp` files are lost upon conversion. | |
73 Additionally, some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms. | |
74 | |
75 For more documentation on the matchms library see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/. | |
76 ]]></help> | |
77 | |
78 | |
79 <expand macro="citations"/> | |
80 </tool> |