<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="FeatureFinderIdentification" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html" category="Quantitation" >
<description><![CDATA[Detects features in MS1 data based on peptide identifications.]]></description>
<manual><![CDATA[Detects features in MS1 data based on peptide identifications.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="FeatureFinderIdentification" description="Detects features in MS1 data based on peptide identifications.">
    <ITEM name="version" value="2.1.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;FeatureFinderIdentification&apos;">
      <ITEM name="in" value="" type="input-file" description="Input file (LC-MS raw data)" required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="id" value="" type="input-file" description="Input file (peptide identifications)" required="true" advanced="false" supported_formats="*.idXML" />
      <ITEM name="out" value="" type="output-file" description="Output file (features)" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="lib_out" value="" type="output-file" description="Output file (assay library)" required="false" advanced="false" supported_formats="*.traML" />
      <ITEM name="chrom_out" value="" type="output-file" description="Output file (chromatograms)" required="false" advanced="false" supported_formats="*.mzML" />
      <ITEM name="trafo_out" value="" type="output-file" description="Output file (RT transformation)" required="false" advanced="false" supported_formats="*.trafoXML" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
      <NODE name="extract" description="Parameters for ion chromatogram extraction">
        <ITEM name="reference_rt" value="adapt" type="string" description="Method for selecting the reference RT, if there are multiple IDs for a peptide and charge. &apos;adapt&apos;: adapt (extend) RT windows based on IDs; &apos;score&apos;: RT of the best-scoring ID; &apos;intensity&apos;: RT of the ID with the most intense precursor; &apos;median&apos;: median RT of all IDs; &apos;all&apos;: no single reference, use RTs of all IDs (requires further processing of results)." required="false" advanced="false" restrictions="adapt,score,intensity,median,all" />
        <ITEM name="rt_window" value="60" type="double" description="RT window size (in sec.) for chromatogram extraction." required="false" advanced="false" restrictions="0:" />
        <ITEM name="mz_window" value="10" type="double" description="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" required="false" advanced="false" restrictions="0:" />
        <ITEM name="isotope_pmin" value="0.03" type="double" description="Minimum probability for an isotope to be included in the assay for a peptide." required="false" advanced="false" restrictions="0:1" />
      </NODE>
      <NODE name="detect" description="Parameters for detecting features in extracted ion chromatograms">
        <ITEM name="peak_width" value="30" type="double" description="Elution peak width in seconds for smoothing (Gauss filter)" required="false" advanced="false" restrictions="0:" />
        <ITEM name="all_features" value="false" type="string" description="Return all features detected by OpenSWATH for an assay, instead of only the best one. (This requires further processing of the results.)" required="false" advanced="true" restrictions="true,false" />
      </NODE>
      <NODE name="model" description="Parameters for fitting elution models to features">
        <ITEM name="type" value="symmetric" type="string" description="Type of elution model to fit to features" required="false" advanced="false" restrictions="symmetric,asymmetric,none" />
        <ITEM name="add_zeros" value="0.2" type="double" description="Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; &apos;0&apos; to disable." required="false" advanced="true" restrictions="0:" />
        <ITEM name="unweighted_fit" value="false" type="string" description="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" required="false" advanced="true" restrictions="true,false" />
        <ITEM name="no_imputation" value="false" type="string" description="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" required="false" advanced="true" restrictions="true,false" />
        <NODE name="check" description="Parameters for checking the validity of elution models (and rejecting them if necessary)">
          <ITEM name="boundaries" value="0.5" type="double" description="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" required="false" advanced="true" restrictions="0:1" />
          <ITEM name="width" value="10" type="double" description="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; &apos;0&apos; to disable" required="false" advanced="true" restrictions="0:" />
          <ITEM name="asymmetry" value="10" type="double" description="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; &apos;0&apos; to disable" required="false" advanced="true" restrictions="0:" />
        </NODE>
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
