Mercurial > repos > recetox > matchms_add_key

comparison matchms_add_key.xml @ 0:ea00a749ec1f draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:26:04 +0000
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-1:000000000000 0:ea00a749ec1f
1 <tool id="matchms_add_key" name="matchms add key" version="@TOOL_VERSION@+galaxy1" profile="21.09">
2 <description>Set metadata key in MSP to static value</description>
3
4 <macros>
5 <import>macros.xml</import>
6 <import>help.xml</import>
7 </macros>
8
9 <expand macro="creator"/>
10
11 <edam_operations>
12 <edam_operation>operation_2409</edam_operation>
13 </edam_operations>
14 <expand macro="bio.tools"/>
15
16 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
18 </requirements>
19
20 <command detect_errors='aggressive'><![CDATA[
21 python ${matchms_python_cli}
22 ]]></command>
23
24 <configfiles>
25 <configfile name="matchms_python_cli">
26 @init_logger@
27
28 from matchms.importing import load_from_msp
29 from matchms.exporting import save_as_msp
30 spectra = list(load_from_msp("${spectral_library}", metadata_harmonization = "False"))
31 new_spectra = []
32 for spectrum in spectra:
33 spectrum.set("${key}", "${value}")
34 new_spectra.append(spectrum)
35 save_as_msp(new_spectra, "${output}")
36 </configfile>
37 </configfiles>
38
39 <inputs>
40 <param label="Spectra file" name="spectral_library" type="data" format="msp"
41 help="Mass spectral library file to add key." />
42
43 <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be assigned to all spectra records in the MSP." />
44 <param label="Value" name="value" type="text" value="" help="Value of the attribute which will be assigned to all spectra records in the MSP." />
45 </inputs>
46
47 <outputs>
48 <data label="${tool.name} on ${on_string}" name="output" format="msp">
49 </data>
50 </outputs>
51
52 <tests>
53 <test>
54 <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
55 <param name="key" value="tool_used"/>
56 <param name="value" value="matchms"/>
57 <output name="output" file="out_matchms_add_key.msp" ftype="msp"/>
58 </test>
59 </tests>
60
61 <help><![CDATA[
62 Description
63 The tool take MSP file as an input and take as parameters the name of the
64 attribute and its value which will be assigned to all spectra records in the MSP.
65 ]]></help>
66
67 <citations>
68 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
69 </citations>
70 </tool>