<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.1.0" name="MultiplexResolver" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MultiplexResolver.html" category="Utilities" >
<description><![CDATA[Completes peptide multiplets and resolves conflicts within them.]]></description>
<manual><![CDATA[Completes peptide multiplets and resolves conflicts within them.]]></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="MultiplexResolver" description="Completes peptide multiplets and resolves conflicts within them.">
    <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;MultiplexResolver&apos;">
      <ITEM name="in" value="" type="input-file" description="Peptide multiplets with assigned sequence information" required="true" advanced="false" supported_formats="*.consensusXML" />
      <ITEM name="out" value="" type="output-file" description="Complete peptide multiplets." required="true" advanced="false" supported_formats="*.consensusXML" />
      <ITEM name="out_conflicts" value="" type="output-file" description="Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information." required="false" advanced="false" supported_formats="*.consensusXML" />
      <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="algorithm" description="Parameters for the algorithm.">
        <ITEM name="labels" value="[][Lys8,Arg10]" type="string" description="Labels used for labelling the samples. [...] specifies the labels for a single sample. For example#br##br#[][Lys8,Arg10]        ... SILAC#br#[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC#br#[Dimethyl0][Dimethyl6]        ... Dimethyl#br#[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl#br#[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL" required="false" advanced="false" />
        <ITEM name="missed_cleavages" value="0" type="int" description="Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)" required="false" advanced="false" restrictions="0:" />
        <ITEM name="mass_tolerance" value="0.1" type="double" description="Mass tolerance in Da for matching the detected to the theoretical mass shifts." required="false" advanced="true" />
      </NODE>
      <NODE name="labels" description="Isotopic labels that can be specified in section &apos;algorithm:labels&apos;.">
        <ITEM name="Arg6" value="6.0201290268" type="double" description="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Arg10" value="10.0082686" type="double" description="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Lys4" value="4.0251069836" type="double" description="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Lys6" value="6.0201290268" type="double" description="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Lys8" value="8.0141988132" type="double" description="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Leu3" value="3.01883" type="double" description="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Dimethyl0" value="28.0313" type="double" description="Dimethyl  |  H(4) C(2)  |  unimod #36" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Dimethyl4" value="32.056407" type="double" description="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Dimethyl6" value="34.063117" type="double" description="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" required="false" advanced="true" restrictions="0:" />
        <ITEM name="Dimethyl8" value="36.07567" type="double" description="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" required="false" advanced="true" restrictions="0:" />
        <ITEM name="ICPL0" value="105.021464" type="double" description="ICPL  |  H(3) C(6) N O  |  unimod #365" required="false" advanced="true" restrictions="0:" />
        <ITEM name="ICPL4" value="109.046571" type="double" description="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" required="false" advanced="true" restrictions="0:" />
        <ITEM name="ICPL6" value="111.041593" type="double" description="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" required="false" advanced="true" restrictions="0:" />
        <ITEM name="ICPL10" value="115.0667" type="double" description="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" required="false" advanced="true" restrictions="0:" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
