Mercurial > repos > recetox > matchms_convert

annotate matchms_convert.xml @ 3:4216e42a5534 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:21:13 +0000
parents 8c3433c6b39c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
2 <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
3
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
4 <macros>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
5 <import>macros.xml</import>
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
6 <import>help.xml</import>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
7 </macros>
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
8
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
9 <expand macro="creator"/>
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
10
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
11 <edam_operations>
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
12 <edam_operation>operation_3434</edam_operation>
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
13 </edam_operations>
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
14 <expand macro="bio.tools"/>
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
15
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
16 <requirements>
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
18 </requirements>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
19
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
20 <command detect_errors='aggressive'><![CDATA[
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
21 python ${matchms_python_cli}
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
22 ]]></command>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
23
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
24 <configfiles>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
25 <configfile name="matchms_python_cli">
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
26 @init_logger@
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
27
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
28 from matchms.importing import load_from_msp, load_from_mgf, load_from_json
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
29 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
30 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
31 #if $output_file.output_format == "msp"
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
32 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
33 #else
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
34 save_as_${output_file.output_format}(spectra, "${converted_library}")
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
35 #end if
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
36 </configfile>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
37 </configfiles>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
38
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
39 <inputs>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
40 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
41 help="Mass spectral library file to convert." />
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
42
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
43 <param label="Harmonization metadata" name="harmonization_metadata" type="boolean" truevalue="True" falsevalue="False"
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
44 checked="true"
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
45 help="Apply metadata harmonization, parsing certain keys required by additional filters or initializing other attributes. The default is True." />
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
46
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
47 <conditional name="output_file">
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
48 <param label="Spectral library format" name="output_format" type="select"
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
49 help="Output format to convert the spectral library into.">
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
50 <option value="msp" selected="true">msp</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
51 <option value="mgf">mgf</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
52 <option value="json">json</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
53 </param>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
54 <when value="msp">
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
55 <param label="Export peak comments" name="export_peak_comments" type="boolean"
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
56 truevalue="True" falsevalue="False" checked="true"
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
57 help="Retain peak comments from individual peaks after the respective mz and intensity pairs when selected." />
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
58 <param label="Export style" name="export_style" type="select"
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
59 help="Converts the keys to a specific style - see [1] for details.. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'.">
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
60 <option value="matchms" selected="true">matchms</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
61 <option value="massbank">massbank</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
62 <option value="nist">nist</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
63 <option value="riken">riken</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
64 <option value="gnps">gnps</option>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
65 </param>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
66 </when>
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
67 <when value="mgf" />
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
68 <when value="json" />
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
69 </conditional>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
70 </inputs>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
71
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
72 <outputs>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
73 <data label="${tool.name} from ${spectral_library.ext} to ${output_file.output_format} on ${on_string}" name="converted_library" format="msp">
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
74 <change_format>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
75 <when input="output_file.output_format" value="mgf" format="mgf" />
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
76 <when input="output_file.output_format" value="json" format="json" />
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
77 </change_format>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
78 </data>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
79 </outputs>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
80
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
81 <tests>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
82 <test>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
83 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
84 <param name="harmonization_metadata" value="False"/>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
85 <param name="output_format" value="mgf"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
86 <output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
87 </test>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
88 <test>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
89 <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
90 <param name="harmonization_metadata" value="False"/>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
91 <param name="output_format" value="json"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
92 <output name="converted_library" file="convert/json_out.json" ftype="json"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
93 </test>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
94 <test>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
95 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
96 <param name="harmonization_metadata" value="False"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
97 <param name="export_peak_comments" value="False"/>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
98 <param name="output_format" value="msp"/>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
99 <param name="export_style" value="matchms"/>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
100 <output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
101 </test>
2
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
102 <test>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
103 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
104 <param name="harmonization_metadata" value="True"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
105 <param name="export_peak_comments" value="False"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
106 <param name="output_format" value="msp"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
107 <param name="export_style" value="matchms"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
108 <output name="converted_library" file="convert/harmonized_msp_out.msp" ftype="msp"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
109 </test>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
110 <test>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
111 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
112 <param name="harmonization_metadata" value="True"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
113 <param name="export_peak_comments" value="True"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
114 <param name="output_format" value="msp"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
115 <param name="export_style" value="matchms"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
116 <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
8c3433c6b39c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32
recetox
parents: 0
diff changeset
117 </test>
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
118 </tests>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
119
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
120
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
121 <help><![CDATA[
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
122 Description
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
123 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
124 This tool can be used to convert from one library format to another.
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
125 Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
126
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
127 .. rubric:: **Footnotes**
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
128 .. [1] Export styles - see this `table <https://github.com/matchms/matchms/blob/master/matchms/data/export_key_conversions.csv>`_ for supported key conversions and detailed description of the export styles.
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
129
3
4216e42a5534 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 2
diff changeset
130 @HELP_matchms@
0
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
131 ]]></help>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
132
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
133
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
134 <expand macro="citations"/>
ad26d6e15401 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52
recetox
parents:
diff changeset
135 </tool>