Changes between Initial Version and Version 1 of openMS_featureMatching_featureLinker_default


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Timestamp:
Nov 24, 2010, 4:46:20 PM (10 years ago)
Author:
b.hoekman@…
Comment:

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  • openMS_featureMatching_featureLinker_default

    v1 v1  
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     3
     4{{{
     5
     6<?xml version="1.0" encoding="ISO-8859-1"?>
     7<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">
     8  <NODE name="FeatureLinker" description="Groups corresponding features in one map or across maps.">
     9    <ITEM name="version" value="1.7.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
     10    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureLinker&apos;">
     11      <ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: &apos;featureXML&apos;)" tags="input file">
     12      </ITEMLIST>
     13      <ITEM name="out" value="" type="string" description="Output file (valid formats: &apos;consensusXML&apos;)" tags="output file" />
     14      <ITEM name="type" value="unlabeled" type="string" description="Feature grouping algorithm type" restrictions="labeled,unlabeled" />
     15      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
     16      <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
     17      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
     18      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
     19      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for software testing only)" tags="advanced" restrictions="true,false" />
     20      <NODE name="algorithm" description="Algorithm parameters section">
     21        <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:" />
     22        <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:" />
     23        <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:" />
     24        <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" />
     25        <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">
     26          <ITEM name="RT" value="1" type="float" description="RT differences are raised to this power" tags="advanced" restrictions="0.1:" />
     27          <ITEM name="MZ" value="2" type="float" description="MZ differences are raised to this power" tags="advanced" restrictions="0.1:" />
     28        </NODE>
     29        <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.">
     30          <ITEM name="RT" value="100" type="float" description="Maximal allowed distance in RT for a pair" restrictions="0:" />
     31          <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:" />
     32          <ITEM name="MZ_unit" value="Da" type="string" description="Unit of &apos;MZ&apos; parameter" restrictions="Da,ppm" />
     33        </NODE>
     34      </NODE>
     35    </NODE>
     36  </NODE>
     37</PARAMETERS>
     38
     39}}}