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comparison matchms_metadata_export.xml @ 2:f04610d25411 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:24:34 +0000
parents dfdbccfa8753
children 7504a8f93699
comparison
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1:1532aa36c89d 2:f04610d25411
1 <tool id="matchms_metadata_export" name="matchms metadata export " version="0.19.0+galaxy0" profile="21.05"> 1 <tool id="matchms_metadata_export" name="matchms metadata export " version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>extract all metadata from mass spectra file to tabular format</description> 2 <description>extract all metadata from mass spectra file to tabular format</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>help.xml</import>
5 </macros> 6 </macros>
6 <expand macro="creator"/> 7 <expand macro="creator"/>
8 <expand macro="bio.tools"/>
9
7 <requirements> 10 <requirements>
8 <requirement type="package" version="0.19.0">matchms</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
9 </requirements> 12 </requirements>
10 13
11 <command detect_errors='aggressive'><![CDATA[ 14 <command detect_errors='aggressive'><![CDATA[
12 python ${matchms_python_cli} 15 python ${matchms_python_cli}
13 ]]></command> 16 ]]></command>
14 17
15 <configfiles> 18 <configfiles>
16 <configfile name="matchms_python_cli"> 19 <configfile name="matchms_python_cli">
17 import pandas
18 from matchms.importing import load_from_msp, load_from_mgf 20 from matchms.importing import load_from_msp, load_from_mgf
19 from matchms.exporting.metadata_export import export_metadata_as_csv 21 from matchms.exporting.metadata_export import export_metadata_as_csv
20 22
21 spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata)) 23 spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))
22 24
43 <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/> 45 <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"/> 46 <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
45 </test> 47 </test>
46 </tests> 48 </tests>
47 49
48 <help><![CDATA[ 50 <help>
49 Documentation 51 Documentation
50 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`. 52 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. 53 This tool can be used to export the metadata accompanying the actual spectral to a tabular file,
52 54 creating a column for each attribute and a row for each spectrum.
53 During harmonization of metadata, some of the keywords might change during the conversion process to a unified form. 55 All keys which are present in at least one spectrum are contained in the output.
54 56
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/. 57 @HELP_matchms@
56 ]]></help> 58 </help>
57 59
58 <expand macro="citations"/> 60 <expand macro="citations"/>
59 </tool> 61 </tool>