annotate macros.xml @ 5:e7eff0c9baa3 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit c6bc00f50c232c1c7cbb2e6f838c14a0c1c20e05

<macros>
    <token name="@TOOL_VERSION@">v3.5.2</token>
    <xml name="requirements">
        <requirements>
            <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx2</container>
        </requirements>
    </xml>
    <xml name="creator">
        <creator>
            <person
                givenName="Zargham"
                familyName="Ahmad"
                url="https://github.com/zargham-ahmad"
                identifier="0000-0002-6096-224X" />
            <organization
                url="https://www.recetox.muni.cz/"
                email="[e-mail]"
                name="RECETOX MUNI" />
        </creator>
    </xml>
    <xml name="refs">
        <xrefs>
               <xref type="bio.tools">recetox-msfinder</xref>
        </xrefs>
     </xml>
    <xml name="input">
        <param name="input_data" type="data" format="msp" label="Input mass spectral library file to which to add peak annotations."
            help="Formula and InChI (or SMILES) codes are required to be present in the library file" />
    </xml>
    <xml name="parameter">
        <param type="float" value="0.01" name="Ms2Tolerance" label="Ms2Tolerance" help="The mass tolerance used for fragment peak matching and annotation." />
        <param name="IsTmsMeoxDerivative" type="boolean" checked="False" truevalue="True" falsevalue="False" label="IsTmsMeoxDerivative"
            help="Check TMS-MeOX derivative to use EIMS database; otherwise, MSMS database is used." />
        <param type="integer" value="1" min="0" max="100" name="RelativeAbundanceCutOff" label="RelativeAbundanceCutOff"
            help="Remove peaks with less than specified % relative intensity from the spectra." />
        <param type="float" value="0.001" name="Ms1Tolerance" label="Ms1Tolerance" help="The precursor m/z tolerance to generate formula candidates." />
        <param type="select" name="MassToleranceType" label="MassToleranceType" help="Da stands for Daltons (amu), and Ppm stands for parts per million">
            <option value="Da" selected="True">Da</option>
            <option value="Ppm">Ppm</option>
        </param>
        <param type="integer" value="-1" name="StructurePredictionTimeOut" label="StructurePredictionTimeOut" help="Time out parameter, value of -1 means no timeout" />
        <param name="LewisAndSeniorCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="LEWIS and SENIOR rules check"
            help="Generate formula candidates that match the valence rules of formula elements. For an explanation of those rules see 'Seven Golden Rules for heuristic 
            filtering of molecular formulas obtained by accurate mass spectrometry'" />
        <param name="element_ratio_check" type="select" value="CommonRange=TRUE" label="element ratio check." 
            help="Generate formula candidates that satisfy every element ratios (ex. H/C ratio should be between 0 and 3.33 for Common range (99.7%) restriction.)">
            <option value="CommonRange=TRUE" selected="true">Common Range</option>
            <option value="ExtendedRange=TRUE">Extended Range</option>
            <option value="ExtremeRange=TRUE">No restriction</option>
        </param>
        <param type="integer" value="2" min="1" max="3" name="TreeDepth" label="Tree Depth"
            help="The limitation of in silico cleavages, i.e. if the user sets '2', the MS-FINDER program generates fragments up to the second level of product ions."/>
        <param type="integer" value="20" min="0" max="100" name="IsotopicAbundanceTolerance" label="Isotopic Ratio Tolerance"
            help="Calculate the isotopic score. The tolerance should be utilized as the sigma value for the Gaussian scoring."/>
        <param name="ElementProbabilityCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="Element probability check"
            help="Generate formula candidates that satisfy the heuristic rules as described in the Seven Golden Rules paper. For example, if a formula 
            candidate contains the following element counts, i.e. NOPS all > 1, the element counts of N, O, P, and S should be less than 9, 19, 3, and 2, respectively."/>
        <param name="IsUseEiFragmentDB" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Use EI fragment database"
            help="Utilize the fragment ion library for EI-MS spectral mining"/>
    </xml>

    <xml name="element_select">
        <option value="Ocheck=True">Oxygen check</option>
        <option value="Ncheck=True">Nitrogen check</option>
        <option value="Pcheck=True">Phosphorus check</option>
        <option value="Scheck=True">Sulfur check</option>
        <option value="Fcheck=True">Fluorine check</option>
        <option value="ClCheck=True">Chlorine Check</option>
        <option value="BrCheck=True">Bromine Check</option>
        <option value="Icheck=True">Iodine check</option>
        <option value="SiCheck=True">Silicon Check</option>
    </xml>

    <xml name="output">
        <collection type="list" format="txt" name="output" label="${tool.name} on ${on_string}">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.smi" directory="output" ext="smi" />
            <discover_datasets  pattern="(?P&lt;designation&gt;.+)\.msp" directory="output" ext="msp" />
        </collection>
    </xml>

    <token name="@HELP@"><![CDATA[
        **Description**

        MS-FINDER was launched as a universal program for compound annotation that supports EI-MS (GC/MS) and 
        MS/MS spectral mining. MS-FINDER provide solution for fragment annotations. The program can annotate 
        your unknowns by the public spectral databases such as MassBank, LipidBlast, and GNPS. MS-FINDER has 
        been developed as the collaborative work between Prof. Masanori Arita team (RIKEN, Reifycs Inc.) and 
        Prof. Oliver Fiehn team (UC Davis) supported by the JST/NSF SICORP Metabolomics for the low carbon society 
        project.

        This galaxy wrapper only peforms MS2 peak annotation given a correctly formatted mass spectral library file.
        FORMULA, PRECURSORMZ and SMILES (or INCHI) metadata entries are required to be present in the input mass spectral library file.
        Each spectrum has to be separated by a single blank line.

        For detailed documentation of the tool please visit https://systemsomicslab.github.io/mtbinfo.github.io/MS-FINDER/tutorial
    ]]>
    </token>

    <xml name="citations">
        <citation type="doi">10.1021/acs.analchem.6b00770</citation>
    </xml>
</macros>