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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="TextExporter" description="Exports various XML formats to a text file.">
<ITEM name="version" value="1.10.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'TextExporter'">
<ITEM name="in" value="" type="string" description="Input file " tags="input file,required" supported_formats="*.featureXML,*.consensusXML,*.idXML,*.mzML" />
<ITEM name="out" value="TextExporter_2_consensus_tsv.tmp" type="string" description="Output file (mandatory for featureXML and idXML)" tags="output file" supported_formats="*.csv" />
<ITEM name="separator" value="" type="string" description="The used separator character(s); if not set the 'tab' character is used" />
<ITEM name="replacement" value="_" type="string" description="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" />
<ITEM name="quoting" value="none" type="string" description="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" restrictions="none,double,escape" />
<ITEM name="no_ids" value="true" type="string" description="Supresses output of identification data." restrictions="true,false" />
<ITEM name="log" value="TOPP.log" 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="true" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="feature" description="Options for featureXML input files">
<ITEM name="minimal" value="false" type="string" description="Set this flag to write only three attributes: RT, m/z, and intensity." restrictions="true,false" />
</NODE>
<NODE name="id" description="Options for idXML input files">
<ITEM name="proteins_only" value="false" type="string" description="Set this flag if you want only protein information from an idXML file" restrictions="true,false" />
<ITEM name="peptides_only" value="false" type="string" description="Set this flag if you want only peptide information from an idXML file" restrictions="true,false" />
<ITEM name="first_dim_rt" value="false" type="string" description="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)." restrictions="true,false" />
</NODE>
<NODE name="consensus" description="Options for consensusXML input files">
<ITEM name="centroids" value="TextExporter_2_consensus_centroids.tmp" type="string" description="Output file for centroids of consensus features" tags="output file" supported_formats="*.csv" />
<ITEM name="elements" value="TextExporter_2_consensus_elements.tmp" type="string" description="Output file for elements of consensus features" tags="output file" supported_formats="*.csv" />
<ITEM name="features" value="TextExporter_2_consensus_features.tmp" type="string" description="Output file for consensus features and contained elements from all maps (writes 'nan's if elements are missing)" tags="output file" supported_formats="*.csv" />
<ITEM name="sorting_method" value="RT_then_MZ" type="string" description="Sorting options can be combined. The precedence is: sort_by_size, sort_by_maps, sorting_method" restrictions="none,RT,MZ,RT_then_MZ,intensity,quality_decreasing,quality_increasing" />
<ITEM name="sort_by_maps" value="true" type="string" description="Apply a stable sort by the covered maps, lexicographically" restrictions="true,false" />
<ITEM name="sort_by_size" value="true" type="string" description="Apply a stable sort by decreasing size (i.e., the number of elements)" restrictions="true,false" />
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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