view isolib.xml @ 4:2b1118bce0b1 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307

<tool id="isolib" name="isolib" version="2.6+galaxy0" profile="21.09">
    <description>create an isotopic pattern library for given compounds and adducts based on enviPat</description>
    <creator>
        <person
            givenName="Helge"
            familyName="Hecht"
            url="https://github.com/hechth"
            identifier="0000-0001-6744-996X" />
        <organization
            url="https://www.recetox.muni.cz/"
            email="[e-mail]"
            name="RECETOX MUNI" />
    </creator>
    <edam_operations>
        <edam_operation>operation_3632</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="1.10.0">bioconductor-metabocoreutils</requirement>
        <requirement type="package" version="1.12.0">bioconductor-spectra</requirement>
        <requirement type="package" version="1.6.0">bioconductor-msbackendmsp</requirement>
        <requirement type="package" version="2.6">r-envipat</requirement>
        <requirement type="package" version="2.1.5">r-readr</requirement>
        <requirement type="package" version="1.3.1">r-tidyr</requirement>
        <requirement type="package" version="1.5.1">r-stringr</requirement>
        <requirement type="package" version="1.0.2">r-purrr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${__tool_directory__}/isolib.R'
            '${input_file}'
            '${ionization.adducts}'
            '${threshold}'
            '${append_adduct}'
            #if $formatting.out_format == "tabular"
            '${formatting.append_isotopes}'
            #else
            'FALSE'
            #end if
            '${formatting.out_format}'
            '${isotope_library}'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Table with input compounds"/>
        <conditional name="ionization">
            <param name="ionization" type="select" label="Ionization mode" help="Ionization mode used in the experiment">
                <option value="negative" selected="true">negative</option>
                <option value="positive">positive</option>
            </param>
            <when value="positive">
                <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
                    <option value="M+H" selected="true">M+H</option>
                </param>
            </when>
            <when value="negative">
                <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
                    <option value="M-H" selected="true">M-H</option>
                    <option value="M-2H">M-2H</option>
                    <option value="2M-H">2M-H</option>
                </param>
            </when>
        </conditional>
        <param name="threshold" type="float" min="0" max="100" value="1" label="Threshold" help="Probability threshold to use as cutoff for isotopic pattern distribution - this can be used to remove low abundant peaks and improve computation performance." />
        <param name="append_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Append adduct to compound name" help="Append the adduct string to the compound name for easy identification." />
        <conditional name="formatting">
            <param name="out_format" type="select" label="Output Format" help="Choose the output format, either MSP or Tabular">
                <option value="tabular">tabular</option>
                <option value="msp" selected="true">msp</option>
            </param>
            <when value="tabular">
                <param name="append_isotopes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Append isotopes to formula" help="Append the isotopic composition to the formula for easy identification." />
            </when>
            <when value="msp">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="msp" name="isotope_library">
            <change_format>
                <when input="formatting.out_format" value="msp" format="msp" />
                <when input="formatting.out_format" value="tabular" format="tabular" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input_file" value="lc_markers_neg.tsv"/>
            <output name="isotope_library" file="test0.msp"/>
        </test>
        <test>
            <param name="input_file" value="markers_no_rt.tsv"/>
            <output name="isotope_library" file="test1.msp"/>
        </test>
        <test>
            <param name="input_file" value="lc_markers_neg.tsv"/>
            <param name="out_format" value="tabular"/>
            <param name="append_isotopes" value="TRUE" />
            <output name="isotope_library" file="test2.tabular"/>
        </test>
        <test>
            <param name="input_file" value="lc_markers_neg.tsv"/>
            <param name="out_format" value="tabular"/>
            <param name="adducts" value="M-H,2M-H"/>
            <output name="isotope_library" file="test3.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool computes isotopic patterns for given compounds and adduct forms.
        The compound table input file should contain the following columns:
        - name: compound name
        - formula: compound formula
        - rt (optional): retention time

        The output is a spectral library in the MSP format.
    ]]></help>
    <citations>
        <citation type="doi">10.1021/acs.analchem.5b00941</citation>
        <citation type="doi">10.3390/metabo12020173</citation>
    </citations>
</tool>