Mercurial > repos > recetox > mfassignr_mfassign
diff macros.xml @ 0:5aa9380f397b draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
author | recetox |
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date | Thu, 15 Aug 2024 12:00:54 +0000 |
parents | |
children | 9cbbfd54d7c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Aug 15 12:00:54 2024 +0000 @@ -0,0 +1,141 @@ +<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" + help= "A numeric value of the intensity cut value being investigated"/> + <param name="mass" type="float" label="mass" + 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>