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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="IsobaricAnalyzer" description="Calculates isobaric quantitative values for peptides">
<ITEM name="version" value="1.11.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'IsobaricAnalyzer'">
<ITEM name="type" value="itraq4plex" type="string" description="Isobaric Quantitation method used in the experiment." restrictions="itraq4plex,itraq8plex,tmt6plex" />
<ITEM name="in" value="" type="string" description="input raw/picked data file " tags="input file,required" supported_formats="*.mzML" />
<ITEM name="out" value="" type="string" description="output consensusXML file with quantitative information" tags="output file,required" supported_formats="*.consensusXML" />
<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="id_pool" value="" type="string" description="ID pool file to DocumentID's for all generated output files. Disabled by default. (Set to 'main' to use /Users/aiche/dev/openms/openms-git/share/OpenMS/IDPool/IDPool.txt)" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="extraction" description="Parameters for the channel extraction.">
<ITEM name="select_activation" value="" type="string" description="Operate only on MSn scans where any of its precursors features a certain activation method (e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering." 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," />
<ITEM name="reporter_mass_shift" value="0.1" type="float" description="Allowed shift (left to right) in Da from the expected position." restrictions="1e-08:0.5" />
</NODE>
<NODE name="itraq4plex" description="Algorithm parameters for itraq4plex">
<ITEM name="channel_114_description" value="l1" type="string" description="Description for the content of the 114 channel." />
<ITEM name="channel_115_description" value="l2" type="string" description="Description for the content of the 115 channel." />
<ITEM name="channel_116_description" value="l3" type="string" description="Description for the content of the 116 channel." />
<ITEM name="channel_117_description" value="lung" type="string" description="Description for the content of the 117 channel." />
<ITEM name="reference_channel" value="114" type="int" description="Number of the reference channel (114-117)." restrictions="114:117" />
<ITEMLIST name="correction_matrix" type="string" description="Override default values (see Documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'">
<LISTITEM value="0.0/1.0/5.9/0.2"/>
<LISTITEM value="0.0/2.0/5.6/0.1"/>
<LISTITEM value="0.0/3.0/4.5/0.1"/>
<LISTITEM value="0.1/4.0/3.5/0.1"/>
</ITEMLIST>
</NODE>
<NODE name="itraq8plex" description="Algorithm parameters for itraq8plex">
<ITEM name="channel_113_description" value="" type="string" description="Description for the content of the 113 channel." />
<ITEM name="channel_114_description" value="" type="string" description="Description for the content of the 114 channel." />
<ITEM name="channel_115_description" value="" type="string" description="Description for the content of the 115 channel." />
<ITEM name="channel_116_description" value="" type="string" description="Description for the content of the 116 channel." />
<ITEM name="channel_117_description" value="" type="string" description="Description for the content of the 117 channel." />
<ITEM name="channel_118_description" value="" type="string" description="Description for the content of the 118 channel." />
<ITEM name="channel_119_description" value="" type="string" description="Description for the content of the 119 channel." />
<ITEM name="channel_121_description" value="" type="string" description="Description for the content of the 121 channel." />
<ITEM name="reference_channel" value="113" type="int" description="Number of the reference channel (113-121). Please note that 120 is not valid." restrictions="113:121" />
<ITEMLIST name="correction_matrix" type="string" description="Override default values (see Documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'">
<LISTITEM value="0.00/0.00/6.89/0.22"/>
<LISTITEM value="0.00/0.94/5.90/0.16"/>
<LISTITEM value="0.00/1.88/4.90/0.10"/>
<LISTITEM value="0.00/2.82/3.90/0.07"/>
<LISTITEM value="0.06/3.77/2.99/0.00"/>
<LISTITEM value="0.09/4.71/1.88/0.00"/>
<LISTITEM value="0.14/5.66/0.87/0.00"/>
<LISTITEM value="0.27/7.44/0.18/0.00"/>
</ITEMLIST>
</NODE>
<NODE name="quantification" description="Parameters for the peptide quantification.">
<ITEM name="isotope_correction" value="true" type="string" description="Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results." restrictions="true,false" />
<ITEM name="normalization" value="false" type="string" description="Enable normalization of channel intensities with respect to the reference channel. The normalization is 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!" restrictions="true,false" />
</NODE>
<NODE name="tmt6plex" description="Algorithm parameters for tmt6plex">
<ITEM name="channel_126_description" value="" type="string" description="Description for the content of the 126 channel." />
<ITEM name="channel_127_description" value="" type="string" description="Description for the content of the 127 channel." />
<ITEM name="channel_128_description" value="" type="string" description="Description for the content of the 128 channel." />
<ITEM name="channel_129_description" value="" type="string" description="Description for the content of the 129 channel." />
<ITEM name="channel_130_description" value="" type="string" description="Description for the content of the 130 channel." />
<ITEM name="channel_131_description" value="" type="string" description="Description for the content of the 131 channel." />
<ITEM name="reference_channel" value="126" type="int" description="Number of the reference channel (126-131)." restrictions="126:131" />
<ITEMLIST name="correction_matrix" type="string" description="Override default values (see Documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '0/0.3/4/0' , '0.1/0.3/3/0.2'">
<LISTITEM value="0.0/0.0/0.0/0.0"/>
<LISTITEM value="0.0/0.0/0.0/0.0"/>
<LISTITEM value="0.0/0.0/0.0/0.0"/>
<LISTITEM value="0.0/0.0/0.0/0.0"/>
<LISTITEM value="0.0/0.0/0.0/0.0"/>
<LISTITEM value="0.0/0.0/0.0/0.0"/>
</ITEMLIST>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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