Version 2 (modified by b.hoekman@…, 8 years ago) (diff)


Module Settings

Module Properties

Author: openMS
Instrument: Default
Data processing step: Feature Matching
Program: OpenMS Feature Linker
Version: 1.7


The default settings u get for unlabeled feature "linking" in OpenMS.


<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="" xmlns:xsi="">
  <NODE name="FeatureLinker" description="Groups corresponding features in one map or across maps.">
    <ITEM name="version" value="1.7.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureLinker&apos;">
      <ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: &apos;featureXML&apos;)" tags="input file">
      <ITEM name="out" value="" type="string" description="Output file (valid formats: &apos;consensusXML&apos;)" tags="output file" />
      <ITEM name="type" value="unlabeled" type="string" description="Feature grouping algorithm type" restrictions="labeled,unlabeled" />
      <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 software testing only)" tags="advanced" restrictions="true,false" />
      <NODE name="algorithm" description="Algorithm parameters section">
        <ITEM name="intensity_exponent" value="0" type="float" description="Intensity ratios are raised to this power.  If set to 0, intensities are not considered." tags="advanced" restrictions="0:" />
        <ITEM name="second_nearest_gap" value="2" type="float" description="The distance for the second nearest neighbors must be larger by this factor than the distance for the matching pair itself" restrictions="1:" />
        <ITEM name="different_charge_penalty" value="1" type="float" description="If charge states are different, distance is multiplied by this factor.  If set to 1, charge has no influence." restrictions="1:" />
        <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" />
        <NODE name="diff_exponent" description="Absolute position differences are raised to this power. E.g. 1 for &apos;linear&apos; distance, 2 for &apos;quadratic&apos; distance">
          <ITEM name="RT" value="1" type="float" description="RT differences are raised to this power" tags="advanced" restrictions="0.1:" />
          <ITEM name="MZ" value="2" type="float" description="MZ differences are raised to this power" tags="advanced" restrictions="0.1:" />
        <NODE name="max_pair_distance" description="Maximal allowed distance for a pair. This uses the sum of the distances in (1.) RT, (2.) MZ, and (3.) the ratio of intensities, (after modification by the corresponding diff_exponent and the intensity_exponent), and (4.) whether the charge states are equal.">
          <ITEM name="RT" value="100" type="float" description="Maximal allowed distance in RT for a pair" restrictions="0:" />
          <ITEM name="MZ" value="0.3" type="float" description="Maximal allowed distance in MZ for a pair [Unit defined by &apos;mz_unit&apos;]" restrictions="0:" />
          <ITEM name="MZ_unit" value="Da" type="string" description="Unit of &apos;MZ&apos; parameter" restrictions="Da,ppm" />