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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="FeatureLinkerUnlabeledQT" description="Groups corresponding features from multiple maps.">
<ITEM name="version" value="1.9.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'FeatureLinkerUnlabeledQT'">
<ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: 'featureXML,consensusXML')" tags="input file,required">
</ITEMLIST>
<ITEM name="out" value="" type="string" description="Output file (valid formats: 'consensusXML')" tags="output file,required" />
<ITEM name="keep_subelements" value="true" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." restrictions="true,false" />
<ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="algorithm" description="Algorithm parameters section">
<ITEM name="use_identifications" value="false" type="string" description="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." restrictions="true,false" />
<ITEM name="ignore_charge" value="false" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" />
<NODE name="distance_RT" description="Distance component based on RT differences">
<ITEM name="max_difference" value="100" type="float" description="Maximum allowed difference in RT" restrictions="0:" />
<ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" />
<ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" />
</NODE>
<NODE name="distance_MZ" description="Distance component based on m/z differences">
<ITEM name="max_difference" value="0.3" type="float" description="Maximum allowed difference in m/z (unit defined by 'mz_unit')" restrictions="0:" />
<ITEM name="unit" value="Da" type="string" description="Unit of the 'max_difference' parameter" restrictions="Da,ppm" />
<ITEM name="exponent" value="2" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" />
<ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" />
</NODE>
<NODE name="distance_intensity" description="Distance component based on differences in relative intensity">
<ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" />
<ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" />
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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