annotate recetox_msfinder.xml @ 4:ae66b58846cd draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit ad60bf881a8fd00546909c76d65ea3c6b65a4fe9

<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3">
    <description>Annotation of fragment peaks in mass spectral libraries.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="refs"/>
    <expand macro="creator" />

    <expand macro="requirements" />
    <command>
        <![CDATA[
        mkdir output;
        sh ${write_param};
        mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp';
        [ -s output/result.msp ] || rm output/result.msp;

    ]]>
    </command>

    <configfiles>
        <configfile name="write_param">
            printf "%s\n" "Ms2Tolerance=$Ms2Tolerance" \
            "IsTmsMeoxDerivative=$IsTmsMeoxDerivative" \
            "RelativeAbundanceCutOff=$RelativeAbundanceCutOff" \
            "Ms1Tolerance=$Ms1Tolerance" \
			"MassToleranceType=$MassToleranceType" \
			"StructurePredictionTimeOut=$StructurePredictionTimeOut" \
            "LewisAndSeniorCheck=$LewisAndSeniorCheck" \
			"IsUseRtForFilteringCandidates=False" \
			"RtToleranceForStructureElucidation=2.5" \
			"IsUsePredictedRtForStructureElucidation=False" \
			"Coeff_RtPrediction=-1" \
			"Intercept_RtPrediction=-1" \
			"IsUseRtInchikeyLibrary=True" \
			"IsUsePredictedCcsForStructureElucidation=False" \
			"IsUseCcsForFilteringCandidates=True" \
			"CcsToleranceForStructureElucidation=10" \
			"CanExcuteMS2AdductSearch=False" \
            "IsUseXlogpPrediction=False" >MSFINDER.INI
        </configfile>
    </configfiles>

    <inputs>
        <expand macro="input" />
        <expand macro="parameter" />
        <!-- <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users.">
            <expand macro="element_check_parameter" />
        </section> -->
    </inputs>

    <outputs>
        <expand macro="output" />
    </outputs>

    <tests>
        <test>
            <param name="input_data" value="test.msp" ftype="msp" />
            <output_collection name="output" type="list">
                <element name="result" file="out.msp" lines_diff="16"/>
            </output_collection>
            <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. -->
        </test>
        <test>
            <param name="input_data" value="test_log.msp" ftype="msp" />
            <output_collection name="output" type="list">
                <element name="log_smiles" file="log_smiles.smi" />
            </output_collection>
        </test>
    </tests>

    <help>
        <![CDATA[
            @HELP@
        ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>