<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE knimeNode PUBLIC "-//UNIKN//DTD KNIME Node 2.0//EN" "http://www.knime.org/Node.dtd">
<knimeNode icon="generic_node.png" type="Manipulator">
    <name>FileConverter</name>
    
    <shortDescription>
        Converts between different MS file formats.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Converts between different MS file formats.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html">Web Documentation for FileConverter</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="in_type">Input file type -- default: determined from file extension or content#br#</option>
		<option name="UID_postprocessing">unique ID post-processing for output data.#br#'none' keeps current IDs even if invalid.#br#'ensure' keeps current IDs but reassigns invalid ones.#br#'reassign' assigns new unique IDs.</option>
		<option name="out_type">Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense.</option>
		<option name="TIC_DTA2D">Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions.</option>
		<option name="MGF_compact">Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)</option>
		<option name="write_mzML_index">Add an index to the file when writing mzML files (default: no index)</option>
		<option name="process_lowmemory">Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms.</option>
		<option name="log">Name of log file (created only when specified)</option>
		<option name="debug">Sets the debug level</option>
		<option name="threads">Sets the number of threads allowed to be used by the TOPP tool</option>
		<option name="no_progress">Disables progress logging to command line</option>
		<option name="force">Overwrite tool specific checks.</option>
		<option name="test">Enables the test mode (needed for internal use only)</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta]">Input file to convert. [mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta]</inPort>
		<outPort index="0" name="out [mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv]">Output file [mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv]</outPort>
 </ports>
    <views>
        <view index="0" name="FileConverter Std Output">The text sent to standard out during the execution of FileConverter.</view>
        <view index="1" name="FileConverter Error Output">The text sent to standard error during the execution of FileConverter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
