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<knimeNode icon="generic_node.png" type="Manipulator">
    <name>XTandemAdapter</name>
    
    <shortDescription>
        Annotates MS/MS spectra using X! Tandem.
    </shortDescription>
    
    <fullDescription>
        <intro><p>Annotates MS/MS spectra using X! Tandem.</p>
		<p>
			<a href="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_XTandemAdapter.html">Web Documentation for XTandemAdapter</a>
		</p>

        </intro>
        
		<option name="version">Version of the tool that generated this parameters file.</option>
		<option name="ignore_adapter_param">The config given in 'default_config_file' is used exclusively! No matter what other parameters (apart from -in,-out,-database,-xtandem_executable) are saying.</option>
		<option name="precursor_mass_tolerance">Precursor mass tolerance</option>
		<option name="fragment_mass_tolerance">Fragment mass error</option>
		<option name="precursor_error_units">Parent monoisotopic mass error units</option>
		<option name="fragment_error_units">Fragment monoisotopic mass error units</option>
		<option name="min_precursor_charge">Minimum precursor charge</option>
		<option name="max_precursor_charge">Maximum precursor charge</option>
		<option name="allow_isotope_error">If set, misassignment to the first and second isotopic 13C peak are also considered.</option>
		<option name="fixed_modifications">Fixed modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</option>
		<option name="variable_modifications">Variable modifications, specified using UniMod (www.unimod.org) terms, e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'</option>
		<option name="missed_cleavages">Number of possible cleavage sites missed by the enzyme</option>
		<option name="minimum_fragment_mz">Minimum fragment mz</option>
		<option name="cleavage_site">The enzyme used for peptide digestion.</option>
		<option name="output_results">Which hits should be reported. All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)</option>
		<option name="max_valid_expect">Maximal E-Value of a hit to be reported (only evaluated if 'output_result' is 'valid' or 'stochastic'</option>
		<option name="refinement">Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag.</option>
		<option name="use_noise_suppression">Enable the use of the noise suppression routines.</option>
		<option name="semi_cleavage">If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag.</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 [mzML]">Input file [mzML]</inPort>
		<inPort index="1" name="database [FASTA]">FASTA file or pro file. Non-existing relative file-names are looked up via'OpenMS.ini:id_db_dir' [FASTA]</inPort>
		<inPort index="2" name="default_config_file [xml]">Default parameters input file, defaulting to the ones in the OpenMS/share folder.All parameters of this adapter take precedence over this file! Use it for parameters not available here! [xml,opt.]</inPort>
		<outPort index="0" name="out [idXML]">Output file [idXML]</outPort>
 </ports>
    <views>
        <view index="0" name="XTandemAdapter Std Output">The text sent to standard out during the execution of XTandemAdapter.</view>
        <view index="1" name="XTandemAdapter Error Output">The text sent to standard error during the execution of XTandemAdapter. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)</view>
    </views>    
</knimeNode>
