comparison matchms_metadata_export.xml @ 12:c01868645f1b draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit da193865f41a3a840ecc4ba0afab1d358554998a

11:cbadbec49b5d

<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>extract all metadata from mass spectra file to tabular format</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>

        python ${matchms_python_cli}
    ]]></command>

<configfiles>
<configfile name="matchms_python_cli">
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>

    </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>

12:c01868645f1b

<tool id="matchms_metadata_export" name="matchms metadata export" version="@TOOL_VERSION@+galaxy1" profile="21.09">
    <description>extract all metadata from mass spectra file to tabular format</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>

        python ${matchms_python_cli}
    ]]></command>

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


if "$harmonize_metadata" == "False":
    matchms.Metadata.set_key_replacements({})

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

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

    </outputs>

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

    <help>