Mercurial > repos > recetox > mfassignr_recallist
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 37faca3342cbcd3bd6b23fe52a00d05151c03bfd
author | recetox |
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date | Fri, 16 Aug 2024 08:27:27 +0000 (4 months ago) |
parents | 6e1813883a9a |
children | ddb9d330ecc0 |
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<macros> <token name="@TOOL_VERSION@">1.0.3</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="GalaxyToolsDevelopmentandDeployment@space.muni.cz" 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"/> <param name="cut" type="float" label="cut" value="0" help= "A numeric value of the intensity cut value being investigated"/> <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="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)" optional="true" 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."/> <param name="SN" type="float" value="0" label="Signal-to-Noise Ratio" help="Sets the noise cut for the data; peaks below this value will not be evaluated."/> <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>