wiki:openMS_featureMatching_featureMatcher_default

Version 3 (modified by b.hoekman@…, 9 years ago) (diff)

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Module Settings

Module Properties

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

Description

The default settings which u get when u run OpenMS MapAligner -write_ini -type pose_clustering_affine.

Settings

<?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="MapAligner" description="Corrects retention time distortions between 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;MapAligner&apos;">
      <ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: &apos;mzML,featureXML,idXML&apos;)" tags="input file">
      </ITEMLIST>
      <ITEMLIST name="out" type="string" description="output files separated by blanks (valid formats: &apos;mzML,featureXML,idXML&apos;)" tags="output file">
      </ITEMLIST>
      <ITEMLIST name="transformations" type="string" description="transformation output files separated by blanks (valid formats: &apos;trafoXML&apos;)" tags="output file">
      </ITEMLIST>
      <ITEM name="type" value="pose_clustering_affine" type="string" description="Map alignment algorithm type" restrictions="apply_given_trafo,identification,pose_clustering_affine,spectrum_alignment" />
      <ITEMLIST name="given_transformations" type="string" description="Transformations to apply by the &apos;apply_given_trafo&apos; algorithm (valid formats: &apos;trafoXML&apos;)" tags="input file">
      </ITEMLIST>
      <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="reference" description="Options to define a reference file (currently only supported by the algorithms &apos;identification&apos; and &apos;pose_clustering_affine&apos;)">
        <ITEM name="file" value="" type="string" description="File to use as reference (for the &apos;pose_clustering_affine&apos; algorithm, same file format as input files required)#br#(valid formats: &apos;mzML,featureXML,idXML&apos;)" tags="input file" />
        <ITEM name="index" value="0" type="int" description="Use one of the input files as reference (&apos;1&apos; for the first file, etc.)" restrictions="0:" />
      </NODE>
      <NODE name="algorithm" description="Algorithm parameters section">
        <ITEM name="symmetric_regression" value="true" type="string" description="If true, linear regression will be based on (y-x) versus (x+y).#br#If false, a &quot;standard&quot; linear regression will be performed for y versus x." restrictions="true,false" />
        <ITEM name="max_num_peaks_considered" value="400" type="int" description="The maximal number of peaks to be considered per map.  This cutoff is only applied to peak maps. To use all peaks, set this to &apos;-1&apos;." restrictions="-1:" />
        <NODE name="superimposer" description="">
          <ITEM name="mz_pair_max_distance" value="0.5" type="float" description="Maximum of m/z deviation of corresponding elements in different maps.  This condition applies to the pairs considered in hashing." restrictions="0:" />
          <ITEM name="rt_pair_distance_fraction" value="0.1" type="float" description="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).  " tags="advanced" restrictions="0:1" />
          <ITEM name="num_used_points" value="2000" type="int" description="Maximum number of elements considered in each map (selected by intensity).  Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1." restrictions="-1:" />
          <ITEM name="scaling_bucket_size" value="0.005" type="float" description="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering.  A good choice for this would be a bit smaller than the error you would expect from repeated runs." restrictions="0:" />
          <ITEM name="shift_bucket_size" value="3" type="float" description="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering.  A good choice for this would be about the time between consecutive MS scans." restrictions="0:" />
          <ITEM name="max_shift" value="1000" type="float" description="Maximal shift which is considered during histogramming.  This applies for both directions." tags="advanced" restrictions="0:" />
          <ITEM name="max_scaling" value="2" type="float" description="Maximal scaling which is considered during histogramming.  The minimal scaling is the reciprocal of this." tags="advanced" restrictions="1:" />
          <ITEM name="dump_buckets" value="" type="string" description="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to.  A serial number for each invocation will be appended automatically." tags="advanced" />
          <ITEM name="dump_pairs" value="" type="string" description="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!).  A serial number for each invocation will be appended automatically." tags="advanced" />
        </NODE>
        <NODE name="pairfinder" description="">
          <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>
          <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" />
          </NODE>
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>