view matchms_remove_key.xml @ 2:0a64e2bcce96 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b797ce0fea5cb3d9a0cf0ec31a21f9b73f112b4e

<tool id="matchms_remove_key" name="matchms remove key" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>Remove metadata entry for all spectra in a library</description>
    
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>

    <expand macro="creator"/>

    <edam_operations>
        <edam_operation>operation_3695</edam_operation>
    </edam_operations>
    <expand macro="bio.tools"/>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

    <command detect_errors='aggressive'><![CDATA[
        python3 '${matchms_python_cli}'
    ]]></command>

<configfiles>
<configfile name="matchms_python_cli">
import matchms
@init_logger@

matchms.Metadata.set_key_replacements({})
key = "${key}".lower()
spectra = list(matchms.importing.load_from_msp("${spectral_library}", metadata_harmonization = "False"))
new_spectra = []
for spectrum in spectra:
    if spectrum.get(key) is not None:
        metadata = spectrum.metadata
        del metadata[key]
        spectrum.metadata = metadata
    new_spectra.append(spectrum)
matchms.exporting.save_as_msp(new_spectra, "${output}")
</configfile>
</configfiles>

    <inputs>
        <param label="Spectra file" name="spectral_library" type="data" format="msp"
            help="Mass spectral library file to add key." />

        <param label="Attribute Name" name="key" type="text" value="" help="Name of the attribute which will be removed from all spectra records in the MSP." />
    </inputs>

    <outputs>
        <data label="${tool.name} on ${on_string}" name="output" format="msp">
        </data>
    </outputs>

    <tests>
        <test>
            <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
            <param name="key" value="ionmode"/>
            <output name="output" file="out_matchms_remove_key.msp" ftype="msp" compare="sim_size"/>
        </test>
    </tests>

    <help><![CDATA[
        Description
        The tool take MSP file as an input and take as parameters the name of the 
        attribute which will be removed from all spectra records in the MSP.
    ]]></help>

    <citations>
        <citation type="doi">10.5281/zenodo.6035335</citation>
    </citations>
</tool>