Version 5 (modified by b.hoekman@…, 2 years ago)

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Module Settings

Module Properties

Author: bhoekman
Instrument: IonTrap
Data processing step: Feature Quantitation
Program: NM-Rules Feature Quantitation
Version: 1.0

Description

Settings as used for the parsing of IonTrap LC-MS chromatograms. These setting will create a relatively small peakList file.

Settings

        <Program program="nmRules" method="nmRules_peakPicking" format="normal">
            <FileSetReferences>
                <FileRef initialFiles="true" program="" method=""/>
            </FileSetReferences>
            <Parameters>
				<!-- binning -->
                <Attribute attributeName="massBinSize" 	value="0.1"/> <!-- massBin size in DA -->

				<!-- Smoothing params !! -->
                <Attribute attributeName="stepSizeRT" 	value="1"/>
                <Attribute attributeName="stepSizeMZ" 	value="10"/> <!-- closer to step count -->
                <Attribute attributeName="meshSigmaRT" 	value="0.15"/>
                <Attribute attributeName="meshSigmaMZ" 	value="0.15"/>
                <Attribute attributeName="factorRT" 	value="4"/>
                <Attribute attributeName="factorMZ" 	value="4"/>

				<!-- PeakPicking Params !! -->
                <Attribute attributeName="M" 		value="5"/>
                <Attribute attributeName="N" 		value="17"/>
                <Attribute attributeName="sliceMove" 	value="10"/>
                <Attribute attributeName="sliceSize"	value="1200"/>
                <Attribute attributeName="threshold" 	value="200"/>

				<!-- optional Params, But give a bit of a speed up -->
                <Attribute attributeName="mzStart" 		value="100"/>
                <Attribute attributeName="mzEnd" 		value="1700"/>

                <Attribute attributeName="transformationFileLocation" value="${GALAXY_DATA_INDEX_DIR}/msCompare/settings/transformations/featureListTransformations.xml"/>
            </Parameters>
        </Program>