annotate matchms_remove_key.xml @ 9:19367db5cf3c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2abca9206b76bf42e6322d751ed3a31a6cc003a4

<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@


#set keys_list = ([str($k.key) for $k in $attribute_repeat])

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

    <inputs>
        <param label="Spectra file" name="spectral_library" type="data" format="msp"
            help="Mass spectral library file to add key." />
        <repeat name="attribute_repeat" title="Keys to remove">
            <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." />
        </repeat>
    </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="remove_key/out_matchms_remove_key.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectral_library" value="filtering/input.msp" ftype="msp"/>
            <repeat name="attribute_repeat">
                <param name="key" value="ionmode"/>
            </repeat>
            <repeat name="attribute_repeat">
                <param name="key" value="spectrumtype"/>
            </repeat>
            <output name="output" file="remove_key/out2_matchms_remove_key.msp" ftype="msp"/>
        </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>