view matchms_metadata_export.xml @ 1:1532aa36c89d draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 41db9f6295985e278fd23b61955bbaecd1f32c32

<tool id="matchms_metadata_export" name="matchms metadata export " version="0.19.0+galaxy0" profile="21.05">
    <description>extract all metadata from mass spectra file to tabular format</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="0.19.0">matchms</requirement>
    </requirements>

    <command detect_errors='aggressive'><![CDATA[
        python ${matchms_python_cli}
    ]]></command>

<configfiles>
<configfile name="matchms_python_cli">
import pandas
from matchms.importing import load_from_msp, load_from_mgf
from matchms.exporting.metadata_export import export_metadata_as_csv

spectra_list = list(load_from_${input_file.ext}("${input_file}", $harmonize_metadata))

export_metadata_as_csv(spectra_list, "${output_file}")
</configfile>
</configfiles>

    <inputs>
        <param label="Spectra file" name="input_file" type="data" format="msp,mgf" help="Mass spectral library file."/>
        <param label="Harmonize metadata" name="harmonize_metadata" type="boolean" truevalue="True" falsevalue="False"
               checked="false" help="Apply harmonization process on the metadata keys (e.g. parse numeric values, derive precursor mass)."/>
    </inputs>

    <outputs>
        <data label="matchms extract metadata on ${on_string}" name="output_file" format="csv"/>
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="convert/mgf_out.mgf" ftype="mgf"/>
            <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
        </test>
        <test>
            <param name="input_file" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
            <output name="output_file" file="convert/metadata.csv" ftype="csv" compare="sim_size" delta="0"/>
        </test>
    </tests>

    <help><![CDATA[
    Documentation
        Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
        This tool can be used to export the metadata accompanying the actual spectral information to a tabular file.

        During harmonization of metadata, some of the keywords might change during the conversion process to a unified form.

        For more documentation on the matchms library see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.
    ]]></help>

    <expand macro="citations"/>
</tool>