view matchms_convert.xml @ 2:49ef4455b0c2 draft

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

<tool id="matchms_convert" name="matchms convert" version="0.19.0+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="0.19.0">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}", ${harmonization_metadata}))
#if $output_file.output_format == "msp"
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
#else
save_as_${output_file.output_format}(spectra, "${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="Harmonization metadata" name="harmonization_metadata" type="boolean" truevalue="True" falsevalue="False"
            checked="true"
            help="Set to False if metadata harmonization to default keys is not desired. The default is True." />

        <conditional name="output_file">
            <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>
            <when value="msp">
                <param label="Export peak comments" name="export_peak_comments" type="boolean"
                    truevalue="True" falsevalue="False" checked="true"
                    help="Writes peak comments to individual peaks after the respective mz/intensity pair when selected." />
                <param label="Export style" name="export_style" type="select"
                    help="Converts the keys to required Export style. One of ['matchms', 'massbank', 'nist', 'riken', 'gnps']. Default is 'matchms'">
                    <option value="matchms" selected="true">matchms</option>
                    <option value="massbank">massbank</option>
                    <option value="nist">nist</option>
                    <option value="riken">riken</option>
                    <option value="gnps">gnps</option>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data label="${tool.name} from ${spectral_library.ext} to ${output_file.output_format} on ${on_string}" name="converted_library" format="msp">
            <change_format>
                <when input="output_file.output_format" value="mgf" format="mgf" />
                <when input="output_file.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="harmonization_metadata" value="False"/>
            <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="harmonization_metadata" value="False"/>
            <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="harmonization_metadata" value="False"/>
            <param name="export_peak_comments" value="False"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="matchms"/>
            <output name="converted_library" file="convert/msp_out.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
            <param name="harmonization_metadata" value="True"/>
            <param name="export_peak_comments" value="False"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="matchms"/>
            <output name="converted_library" file="convert/harmonized_msp_out.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
            <param name="harmonization_metadata" value="True"/>
            <param name="export_peak_comments" value="True"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="matchms"/>
            <output name="converted_library" file="convert/harmonized_msp_peakcomments_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>