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Viewing changes to source/TEST/TOPP/FeatureLinkerUnlabeled_1_parameters.ini

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2012-11-12 15:58:12 UTC
  • Revision ID: package-import@ubuntu.com-20121112155812-vr15wtg9b50cuesg
Tags: upstream-1.9.0
Import upstream version 1.9.0

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source/TEST/TOPP/FeatureLinkerUnlabeled_1_parameters.ini
 
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<?xml version="1.0" encoding="ISO-8859-1"?>
 
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<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">
 
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  <NODE name="FeatureLinkerUnlabeled" description="Groups corresponding features from multiple maps.">
 
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    <ITEM name="version" value="1.9.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
 
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    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureLinkerUnlabeled&apos;">
 
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      <ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: &apos;featureXML,consensusXML&apos;)" tags="input file,required">
 
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      </ITEMLIST>
 
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      <ITEM name="out" value="" type="string" description="Output file (valid formats: &apos;consensusXML&apos;)" tags="output file,required" />
 
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      <ITEM name="keep_subelements" value="false" type="string" description="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output." restrictions="true,false" />
 
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      <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" />
 
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      <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
 
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      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
 
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      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
 
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      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
 
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      <NODE name="algorithm" description="Algorithm parameters section">
 
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        <ITEM name="second_nearest_gap" value="2" type="float" description="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself" restrictions="1:" />
 
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        <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" />
 
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        <ITEM name="ignore_charge" value="true" type="string" description="Compare features normally even if their charge states are different" restrictions="true,false" />
 
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        <NODE name="distance_RT" description="Distance component based on RT differences">
 
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          <ITEM name="max_difference" value="200" type="float" description="Maximum allowed difference in RT" restrictions="0:" />
 
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          <ITEM name="exponent" value="1" type="float" description="Normalized RT differences are raised to this power" tags="advanced" restrictions="0:" />
 
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          <ITEM name="weight" value="1" type="float" description="RT distances are weighted by this factor" tags="advanced" restrictions="0:" />
 
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        </NODE>
 
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        <NODE name="distance_MZ" description="Distance component based on m/z differences">
 
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          <ITEM name="max_difference" value="0.5" type="float" description="Maximum allowed difference in m/z (unit defined by &apos;mz_unit&apos;)" restrictions="0:" />
 
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          <ITEM name="unit" value="Da" type="string" description="Unit of the &apos;max_difference&apos; parameter" restrictions="Da,ppm" />
 
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          <ITEM name="exponent" value="1" type="float" description="Normalized m/z differences are raised to this power" tags="advanced" restrictions="0:" />
 
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          <ITEM name="weight" value="1" type="float" description="m/z distances are weighted by this factor" tags="advanced" restrictions="0:" />
 
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        </NODE>
 
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        <NODE name="distance_intensity" description="Distance component based on differences in relative intensity">
 
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          <ITEM name="exponent" value="1" type="float" description="Differences in relative intensity are raised to this power" tags="advanced" restrictions="0:" />
 
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          <ITEM name="weight" value="0" type="float" description="Distances based on relative intensity are weighted by this factor" tags="advanced" restrictions="0:" />
 
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        </NODE>
 
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      </NODE>
 
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    </NODE>
 
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  </NODE>
 
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</PARAMETERS>