annotate macros.xml @ 4:3b09c6e3013b draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 4bd188e61f09431c0b7e73b35fb8ccf5ee7af6ac

<macros>
    <token name="@TOOL_VERSION@">1.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-mfassignr</requirement>
        </requirements>
    </xml>

    <xml name="refs">
        <xrefs>
               <xref type="bio.tools">mfassignr</xref>
        </xrefs>
    </xml>

    <xml name="creator">
        <creator>
            <person
                givenName="Kristina"
                familyName="Gomoryova"
                url="https://github.com/KristinaGomoryova"
                identifier="0000-0003-4407-3917" />
            <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
            <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="kmdnoise_param">
        <param name="input_file" type="data" format="tabular" label="Input data"
               help= "Input data frame, first column is mass, second column is intensity"/>
        <param name="upper_y" type="float" label="upper limit for the y intercept" value="0.2"
               help= "The upper y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.2, so that it does not interact with any potentially double-charged peaks."/>
        <param name="lower_y" type="float" label="lower limit for the y intercept" value="0.05"
               help="The lower y-intercept value to isolate noise peaks in the equation for the KMD plot: y = 0.001123*x + b. Default value is set to 0.05 to ensure no analyte peaks are incorporated into the noise estimation."/>
        <param name="upper_x" optional="true" type="float" label="upper limit for the x intercept"
               help="If not set, it defaults to maximum mass in the mass spectrum."/>
        <param name="lower_x" optional="true" type="float" label="lower limit for the x intercept"
               help="If not set, it defaults to minimum mass in the mass spectrum."/>
    </xml>

    <xml name="histnoise_param">
        <param name="input_file" type="data" format="tabular" label="Input data"
               help= "Input data frame, first column is mass, second column is intensity"/>
        <param name="SN" type="float" label="signal-to-noise threshold" value="0"
               help= "A numeric value for situations where a predefined noise value is desired, default is 0"/>
        <param name="bin" type="float" label="bindwidth of the histogram" value="0.01"
               help= "A numeric value determining the binwidth of the histogram, default is 0.01"/>
    </xml>

    <xml name="noise_threshold_params">
       <param name="sn_ratio" type="float" label="SN ratio" value="6"
               help= "Noise multiplier. Recommended value is 6."/>
        <param name="kmdn" type="float" label="Estimated noise" value="0"
               help= "Estimated noise, either from the KMDNoise or HistNoise function."/>
    </xml>

    <xml name="snplot_param">
        <param name="input_file" type="data" format="tabular" label="Input data"
               help= "Input data frame, first column is mass, second column is intensity"/>
        <expand macro="noise_threshold_params" />
        <param name="mass" type="float" label="mass" value="300"
               help= "A numeric value setting a centerpoint to look at the mass spectrum"/>
        <param name="window_x" type="float" label="window.x" value="0.5"
               help= "A numeric value setting the +/- range around the mass centerpoint, default is 0.5"/>
        <param name="window_y" type="float" label="window.y" value="10"  
               help= "A numeric value setting the y axis value for the plot, determined by multiplying the cut by this value"/> 
    </xml>

    <xml name="ionmode_param">
       <param name="ionmode" type="select" display="radio" label="Ion mode" help= "The ionization mode.">
              <option value="neg" >negative</option>
              <option value="pos" selected="true">positive</option> 
        </param>
    </xml>

    <xml name="mfassign_param">
        <param name="ppm_err" type="integer" label="ppm_err"
               help= "Error tolerance (ppm) for formula assignment" value="3"/>
        <expand macro="ionmode_param" />
        <expand macro="noise_threshold_params" />
        <param name="lowMW" type="float" label="Lower limit of molecular mass to be assigned" value="100"
               help= "Lower limit of molecular mass to be assigned."/>
        <param name="highMW" type="float" label="Upper limit of molecular mass to be assigned" value="1000"
               help= "Upper limit of molecular mass to be assigned."/>
    </xml>

    <xml name="findrecalseries_param">
        <param name="input_file" type="data" format="tabular" label="Input data"
               help= "Recalibration series, output from RecalList"/>
        <param name="global_min" type="float" label="Global min" value="0" min="0"
               help= "A lower bound of the instrument m/z range."/>
        <param name="global_max" type="float" label="Global max" value="1000" min="0"
               help= "A higher bound of the instrument m/z range."/>
        <param name="number_of_combinations" type="integer" label="Number of combinations"
               help= "Combinations of how many series should be computed." value="5"/>
        <param name="abundance_score_threshold" type="float" label="Abundance score threshold" value="100"
               help= "A threshold for filtering abundance score parameter. The series with higher values are better."/>
        <param name="peak_distance_threshold" type="float" label="Peak distance threshold" value="2"
               help= "A threshold for the peak distance parameter. The closer this value is to 1, the better."/>
        <param name="coverage_threshold" type="integer" label="How many % of the m/z range should be covered."
               help= "How many % of the m/z range should be covered." value="90"/>
        <param name="fill_series" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Whether to return top 10 unique series (TRUE) or series only from the best combination."
               help= "If TRUE, top 10 unique series will be returned, otherwise only the series from the best
               combination will be returned." value="false"/>
    </xml>

    <xml name="recal_param">
        <param name="input_file" type="data" format="tabular" label="Input data (Output from MFAssign)"
               help= "Input data frame, the output from MFAssign or MFAssignCHO"/>
       <param name="series" type="data" format="tabular" label="Calibration series (Output from RecalList)"
               help= "Calibration series (Output from RecalList). At maximum the first 10 rows are used."/>
        <param name="peaks" type="data" format="tabular" label="Peaks dataframe (Mono from IsoFiltR)"
               help= "Peaks data frame, the Mono output from IsoFiltR"/>              
        <param name="isopeaks" type="data" format="tabular" label="Isopeaks dataframe (Iso from IsoFiltR)" 
               help= "Isopeaks data frame, the Mono output from IsoFiltR"/>
        <expand macro="ionmode_param" />
        <expand macro="noise_threshold_params" />
        <param name="mzRange" type="float" label="Mass windows used for the segmented recalibration" value="30"
               help= "Mass windows used for the segmented recalibration"/>
        <param name="step_O" type="float" label="Number of oxygen steps for formula extension" value="3"
               help= "Number of oxygen steps for formula extension"/>
        <param name="step_H2" type="float" label="Number of H2 steps for formula extension" value="5"
               help= "Number of H2 steps for formula extension"/>
         <param name="CalPeak" type="float" label="Maximum allowed recalibrant peaks per mzRange defined segment" value="150" help= "Maximum allowed recalibrant peaks per mzRange defined segment"/>      

    </xml>

    <xml name="isofiltr_param">
        <param name="peaks" type="data" format="tabular" label="Input Peak Data"
        help="The input data frame containing abundance and peak mass."/>
        <expand macro="noise_threshold_params" />
        <param name="Carbrat" type="float" value="60" min="5" label="Maximum 13C/12C Ratio"
        help="Sets the maximum allowed ratio for matching 13C isotopes."/>
        <param name="Sulfrat" type="float" value="30" label="Maximum 34S/32S Ratio"
        help="Sets the maximum allowed ratio for matching 34S isotopes."/>
        <param name="Sulferr" type="float" value="5" label="Maximum Error for 34S Matching (ppm)"
        help="Sets the maximum allowed error (ppm) for 34S mass matching."/>
        <param name="Carberr" type="float" value="5" label="Maximum Error for 13C Matching (ppm)"
        help="Sets the maximum allowed error (ppm) for 13C mass matching."/>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1016/j.envres.2020.110114</citation>
        </citations>        
    </xml>

</macros>