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Viewing changes to source/TEST/TOPP/TMTAnalyzer.ini

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

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source/TEST/TOPP/TMTAnalyzer.ini
 
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<?xml version="1.0" encoding="ISO-8859-1"?>
 
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<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">
 
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  <NODE name="TMTAnalyzer" description="Calculates TMT quantitative values for peptides">
 
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    <ITEM name="version" value="1.10.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
 
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    <NODE name="1" description="Instance &apos;1&apos; section for &apos;TMTAnalyzer&apos;">
 
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      <ITEM name="in" value="" type="string" description="input raw/picked data file " tags="input file,required" restrictions="*.mzML" />
 
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      <ITEM name="out" value="" type="string" description="output consensusXML file with quantitative information" tags="output file,required" restrictions="*.consensusXML" />
 
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      <ITEM name="out_mzq" value="" type="string" description="Optional output file of MzQuantML." tags="advanced,output file" restrictions="*.mzq" />
 
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      <ITEM name="out_stats" value="" type="string" description="output statistics as tab-separated file (readable by R or Excel or ...)" tags="output file" restrictions="*.tsv" />
 
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      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" tags="advanced" />
 
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      <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
 
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      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
 
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      <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
 
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      <ITEM name="id_pool" value="" type="string" description="ID pool file to DocumentID&apos;s for all generated output files. Disabled by default. (Set to &apos;main&apos; to use /Users/aiche/dev/openms/openms-src/share/OpenMS//IDPool/IDPool.txt)" />
 
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      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
 
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      <NODE name="algorithm" description="Algorithm parameters section">
 
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        <NODE name="Extraction" description="">
 
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          <ITEM name="select_activation" value="High-energy collision-induced dissociation" type="string" description="Operate only on MSn scans where any of its precursors features a certain activation method (usually HCD for iTRAQ). Set to empty string if you want to disable filtering.#br#" restrictions="Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation," />
 
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          <ITEM name="reporter_mass_shift" value="0.1" type="float" description="Allowed shift (left to right) in Da from the expected position (of e.g. 114.1, 115.1)" restrictions="1e-08:0.5" />
 
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          <ITEMLIST name="channel_active" type="string" description="Each channel that was used in the experiment and its description (114-117 for 4plex; 113-121 for 8-plex;126-131 for TMT-6-plex) in format &lt;channel&gt;:&lt;name&gt;, e.g. &quot;114:myref&quot;,&quot;115:liver&quot;.">
 
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            <LISTITEM value="126:channel-1"/>
 
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            <LISTITEM value="127:channel-2"/>
 
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            <LISTITEM value="128:channel-3"/>
 
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            <LISTITEM value="129:channel-4"/>
 
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            <LISTITEM value="130:channel-5"/>
 
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            <LISTITEM value="131:channel-6"/>
 
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          </ITEMLIST>
 
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        </NODE>
 
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        <NODE name="Quantification" description="">
 
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          <ITEM name="isotope_correction" value="false" type="string" description="enable isotope correction (highly recommended)" tags="advanced" restrictions="true,false" />
 
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          <ITEM name="do_normalization" value="false" type="string" description="Normalize channels? Done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!" tags="advanced" restrictions="true,false" />
 
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          <ITEM name="channel_reference" value="126" type="int" description="number of the reference channel (114-117 for 4plex)" restrictions="113:131" />
 
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          <NODE name="isotope_correction" description="Isotope correction matrices for 4plex and 8plex. Only one of them will be used (depending on iTRAQ mode)">
 
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            <ITEMLIST name="4plex" type="string" description="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. &apos;114:0/0.3/4/0&apos; , &apos;116:0.1/0.3/3/0.2&apos; " tags="advanced">
 
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              <LISTITEM value="114:0/1/5.9/0.2"/>
 
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              <LISTITEM value="115:0/2/5.6/0.1"/>
 
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              <LISTITEM value="116:0/3/4.5/0.1"/>
 
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              <LISTITEM value="117:0.1/4/3.5/0.1"/>
 
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            </ITEMLIST>
 
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            <ITEMLIST name="8plex" type="string" description="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. &apos;114:0/0.3/4/0&apos; , &apos;116:0.1/0.3/3/0.2&apos; " tags="advanced">
 
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              <LISTITEM value="113:0/0/6.89/0.22"/>
 
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              <LISTITEM value="114:0/0.94/5.9/0.16"/>
 
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              <LISTITEM value="115:0/1.88/4.9/0.1"/>
 
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              <LISTITEM value="116:0/2.82/3.9/0.07"/>
 
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              <LISTITEM value="117:0.06/3.77/2.99/0"/>
 
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              <LISTITEM value="118:0.09/4.71/1.88/0"/>
 
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              <LISTITEM value="119:0.14/5.66/0.87/0"/>
 
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              <LISTITEM value="121:0.27/7.44/0.18/0"/>
 
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            </ITEMLIST>
 
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            <ITEMLIST name="tmt-6plex" type="string" description="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ; e.g. &apos;126:0/0.3/4/0&apos; , &apos;128:0.1/0.3/3/0.2&apos; " tags="advanced">
 
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              <LISTITEM value="126:0/0/0/0"/>
 
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              <LISTITEM value="127:0/0/0/0"/>
 
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              <LISTITEM value="128:0/0/0/0"/>
 
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              <LISTITEM value="129:0/0/0/0"/>
 
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              <LISTITEM value="130:0/0/0/0"/>
 
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              <LISTITEM value="131:0/0/0/0"/>
 
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            </ITEMLIST>
 
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          </NODE>
 
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        </NODE>
 
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        <NODE name="MetaInformation" description="">
 
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          <ITEM name="Program" value="OpenMS::TMTAnalyzer" type="string" description="" tags="advanced" />
 
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        </NODE>
 
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      </NODE>
 
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    </NODE>
 
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  </NODE>
 
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</PARAMETERS>