comparison matchms_formatter.xml @ 32:604131c54f97 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit bd80a813fb2f01f22eed0c874f8911ce4d00762a

31:a5a5b147da70

<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>reformat scores object of matchms to long format table</description>

    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>

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

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
        <requirement type="package" version="1.1.4">pandas</requirement>
    </requirements>

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

    <inputs>
        <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
        <param label="Key" name="key" type="text" value="compound_name" help="Name of the key to use. Default is 'compound_name'." />
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}" name="output" format="tsv"/>
    </outputs>

    <tests>
        <test>
            <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
            <param name="key" value="compound_name"/>
            <output name="output" value="formatter/fill2_formatted.tsv" ftype="tsv"
                checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
        </test>
        <test>
            <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
            <param name="key" value="compound_name"/>
            <output name="output" file="formatter/test4_formatted.tsv" ftype="tsv"/>
        </test>
    </tests>

    <help>
        @HELP_formatter@

32:604131c54f97

<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT">
    <description>reformat scores object of matchms to long format table</description>

    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>

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

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

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

    <inputs>
        <param label="Scores object" name="scores" type="data" format="json" help="matchms Scores json file." />
        <param label="Key" name="key" type="text" value="compound_name" help="Name of the key to use. Default is 'compound_name'." />
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}" name="output" format="tabular"/>
    </outputs>

    <tests>
        <test>
            <param name="scores" value="formatter/fill2_trunc_scores_with_metadata_match.json" ftype="json"/>
            <param name="key" value="compound_name"/>
            <output name="output" value="formatter/fill2_formatted.tsv" ftype="tabular"
                checksum="md5$4f0d83da381b8a403d807d26a9dd0f34"/>
        </test>
        <test>
            <param name="scores" value="similarity/scores_test4_out.json" ftype="json"/>
            <param name="key" value="compound_name"/>
            <output name="output" file="formatter/test4_formatted.tsv" ftype="tabular"/>
        </test>
    </tests>

    <help>
        @HELP_formatter@