annotate mfassignr_isofiltr.xml @ 6:b880fcae60ea draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 1e98df2131b9b5384ca2e4310f93270eae6f517c

<tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy1" profile="23.0">
    <description>Separates likely isotopic masses from monoisotopic masses in a mass list</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_3172</edam_topic>    
    </edam_topics>
    <edam_operations>  
        <edam_operation>operation_3629</edam_operation>  
    </edam_operations>
    <expand macro="creator" />
    <expand macro="refs" />

    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${mfassignr_isofiltr}'
    ]]>
    </command>
    <configfiles>
        <configfile name="mfassignr_isofiltr"><![CDATA[
            peaks <- read.table("$peaks", header=TRUE, sep="\t")
            SN = $sn_ratio * $kmdn

            result <- MFAssignR::IsoFiltR(
                peaks = peaks,
                SN = SN,
                Carbrat = $Carbrat,
                Sulfrat = $Sulfrat,
                Sulferr = $Sulferr,
                Carberr = $Carberr
            )
            
            write.table(result[["Mono"]], file="$mono_out", sep="\t", row.names=FALSE)
            write.table(result[["Iso"]], file="$iso_out", sep="\t", row.names=FALSE)
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="isofiltr_param"/>
    </inputs>
    <outputs>
        <data name="mono_out" format="tabular" label="Monoisotopic Masses"/>
        <data name="iso_out" format="tabular" label="Isotopic Masses"/>
    </outputs>
    <tests>
        <test>
            <param name="peaks" value="QC1_1_POS_500.tabular" ftype="tabular"/>
            <output name="mono_out" file="isofiltr/mono_out.tabular" ftype="tabular"/>
            <output name="iso_out" file="isofiltr/iso_out.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
        IsoFiltR identifies and separates likely isotopic masses from monoisotopic masses in a mass list. 
        This should be done prior to formula assignment to reduce incorrect formula assignments.
        
        The input is a table containing abundance and peak mass in the following format:

        +--------------------+-------------------+------------------------+
        | mz                 | area              | rt                     |
        +====================+===================+========================+
        | 110.03486266079899 | 3410926.862054969 | 190.03735922916195     |
        +--------------------+-------------------+------------------------+
        | 110.05988136843429 | 7658687.858       | 241.17645551084158     |
        +--------------------+-------------------+------------------------+
        | ...                | ...               | ...                    |
        +--------------------+-------------------+------------------------+
    </help>
    <expand macro="citations"/>
</tool>