<?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>FileMerger</name>
    
    <shortDescription>
        Merges several MS files into one file.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Merges several MS files into one file.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileMerger.html">Web Documentation for FileMerger</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)</option>
		<option name="annotate_file_origin">Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only).</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>
		<option name="gap">The amount of gap (in seconds) to insert between the RT ranges of different input files. RT concatenation is enabled if a value &gt; 0 is set.</option>
		<option name="rt_auto">Assign retention times automatically (integers starting at 1)</option>
		<option name="rt_custom">List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of input files.</option>
		<option name="rt_filename">Try to guess the retention time of a file based on the filename. This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'</option>
		<option name="ms_level">If 1 or higher, this number is assigned to spectra as the MS level. This option is useful for DTA files which do not contain MS level information.</option>

    </fullDescription>
    
    <ports>
		<inPort index="0" name="in [mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML]">Input files separated by blank [mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML]</inPort>
		<outPort index="0" name="out [mzML,featureXML,consensusXML,traML]">Output file [mzML,featureXML,consensusXML,traML]</outPort>
		<outPort index="1" name="trafo_out [trafoXML,Inactive]">Output of retention time transformations that were applied to the input files to produce non-overlapping RT ranges. If used, one output file per input file is required. [trafoXML,Inactive]</outPort>
 </ports>
    <views>
        <view index="0" name="FileMerger Std Output">The text sent to standard out during the execution of FileMerger.</view>
        <view index="1" name="FileMerger Error Output">The text sent to standard error during the execution of FileMerger. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
