annotate matchms_convert.xml @ 0:f0ad1b8685fd draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8989605190816b606fd0bf5be101c6d385a4ce52

<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>convert between mass spectral library formats using matchms</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

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

<configfiles>
<configfile name="matchms_python_cli">
from matchms.importing import load_from_msp, load_from_mgf, load_from_json
from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
spectra = list(load_from_${spectral_library.ext}("${spectral_library}", False))
#if $output_format == "msp"
save_as_msp(spectra, "${converted_library}", write_peak_comments = False)
#else
save_as_${output_format}(spectra, "${converted_library}")
#end if
</configfile>
</configfiles>

    <inputs>
        <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json" help="Mass spectral library file to convert." />

        <param label="Spectral library format" name="output_format" type="select"
            help="Output format to convert the spectral library into.">
            <option value="msp" selected="true">msp</option>
            <option value="mgf">mgf</option>
            <option value="json">json</option>
        </param>
    </inputs>

    <outputs>
        <data label="${tool.name} from ${spectral_library.ext} to ${output_format} on ${on_string}" name="converted_library" format="msp">
            <change_format>
                <when input="output_format" value="mgf" format="mgf" />
                <when input="output_format" value="json" format="json" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
            <param name="output_format" value="mgf"/>
            <output name="converted_library" file="convert/mgf_out.mgf" ftype="mgf"/>
        </test>
        <test>
            <param name="spectral_library" value="similarity/RECETOX_Exposome_pesticides_HR_MS_20220323.msp" ftype="msp"/>
            <param name="output_format" value="json"/>
            <output name="converted_library" file="convert/json_out.json" ftype="json"/>
        </test>
        <test>
            <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
            <param name="output_format" value="msp"/>
            <output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
        </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 convert from one library format to another.

        Please note that peak comments in `RIKEN` style `msp` files are lost upon conversion.
        Additionally, some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.

        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>