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October 4, 2018 13:56
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Updated TOPPAS workflow for the IgG data set
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| <?xml version="1.0" encoding="ISO-8859-1"?> | |
| <PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> | |
| <NODE name="info" description=""> | |
| <ITEM name="version" value="2.3.0" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="num_vertices" value="15" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="num_edges" value="16" type="int" description="" required="false" advanced="false" /> | |
| <ITEM name="description" value="<![CDATA[]]>" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="vertices" description=""> | |
| <NODE name="0" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| <LISTITEM value="H:/Data/MSData/input/rawfiles/20160417_MH_IgG_FASP_Tryp_HILIC_Enri_HCDstep.mzML"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-300" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-300" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| <LISTITEM value="H:/Data/MSData/input/FASTA Files/IgG_1_2_3_4.fasta"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="360" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="input file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEMLIST name="file_names" type="string" description="" required="false" advanced="false"> | |
| <LISTITEM value="H:/Data/MSData/input/GlycanDB/IgG_compositions.txt"/> | |
| </ITEMLIST> | |
| <ITEM name="x_pos" value="-400" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="560" type="double" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="PeakPickerHiRes" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-20" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="input profile data file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="output peak file " required="true" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="processOption" value="inmemory" type="string" description="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" required="false" advanced="true" restrictions="inmemory,lowmemory" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="algorithm" description="Algorithm parameters section"> | |
| <ITEM name="signal_to_noise" value="1" type="double" description="Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="spacing_difference_gap" value="4" type="double" description="The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="spacing_difference" value="1.5" type="double" description="Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" /> | |
| <ITEM name="missing" value="1" type="int" description="Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms." required="false" advanced="true" restrictions="0:" /> | |
| <ITEMLIST name="ms_levels" type="int" description="List of MS levels for which the peak picking is applied. Other scans are copied to the output without changes." required="false" advanced="false" restrictions="1:"> | |
| <LISTITEM value="1"/> | |
| <LISTITEM value="2"/> | |
| </ITEMLIST> | |
| <NODE name="SignalToNoise" description=""> | |
| <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" /> | |
| <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" /> | |
| <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" /> | |
| <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="FileBuilder" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-20" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="FileBuilder" type="string" description="Which external tool configuration to load?! See '/scratch/glyxsuite/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,GlycanCompositionBuilder,GlycopetideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,PeptideFilter,PeptideSearch,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should pointto share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="inOriginal" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="inReplace" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="out" value="" type="output-file" description="" required="false" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="MSLevel" value="2" type="int" description="MSLevel spectra to be replaced by replacement file" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="460" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-20" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-380" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="160" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="output file list" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="440" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="620" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="output_folder_name" value="" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="FeatureFinderMS" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="160" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="FeatureFinderMS" type="string" description="Which external tool configuration to load?! See '/scratch/glyxsuite/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,GlycanCompositionBuilder,GlycopetideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,PeptideFilter,PeptideSearch,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="inMZML" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="outFeature" value="" type="output-file" description="" required="false" advanced="false" supported_formats="*.featureXML" /> | |
| <ITEM name="tolerance" value="0.1" type="double" description="Mass tolerance in Da" required="false" advanced="false" /> | |
| <ITEM name="mswindow" value="4" type="double" description="Precursor mass window in Da" required="false" advanced="false" /> | |
| <ITEM name="precursorshift" value="3" type="double" description="Allowed precursor mass shift to search best precurosr candidate" required="false" advanced="false" /> | |
| <ITEM name="rtwindow" value="30" type="double" description="RT range of an eluting peak in seconds" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="glyxFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="160" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="glyxFilter" type="string" description="Which external tool configuration to load?! See '/afs/mpi-magdeburg.mpg.de/home/pioch/Data/software/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,FragmentationTypeFilesplitter,GlycanCompositionBuilder,GlycoDomainViewer,GlycoIdentificationScore,GlycopetideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,RAWFileConvert,PeptideFilter,QCMLExport,RAWDirConvert,RobustPeakPicker,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="inMZML" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.mzML" /> | |
| <ITEM name="inFeature" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.featureXML" /> | |
| <ITEM name="outGlyML" value="" type="output-file" description="" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="createFeatures" value="true" type="string" description="Create features for featureless spectra" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="hasFucose" value="true" type="string" description="Check for oxonium ions containing fucose" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="hasNANA" value="true" type="string" description="Include oxoniumions indicative for sialisation with NANA" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="hasNGNA" value="false" type="string" description="Include oxoniumions indicative for sialisation with NGNA" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="oxoniumions" value="" type="string" description="Check for additional oxonium ions" required="false" advanced="false" /> | |
| <ITEM name="tolerance" value="0.05" type="double" description="Mass tolerance" required="false" advanced="false" /> | |
| <ITEM name="toleranceType" value="Da" type="string" description="Type of the given mass tolerance" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="ionthreshold" value="0" type="int" description="Threshold for reporter ion intensity to be counted for score" required="false" advanced="false" /> | |
| <ITEM name="scorethreshold" value="1.7" type="double" description="score threshold for reporting mass spectrum as glycopeptide" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="GlycopeptideMatcher" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="400" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="GlycopeptideMatcher" type="string" description="Which external tool configuration to load?! See '/afs/mpi-magdeburg.mpg.de/home/pioch/Data/software/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,FragmentationTypeFilesplitter,GlycanCompositionBuilder,GlycoDomainViewer,GlycoIdentificationScore,GlycopetideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,RAWFileConvert,PeptideFilter,QCMLExport,RAWDirConvert,RobustPeakPicker,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="out" value="" type="output-file" description="File output Analysis file with appended Glycopeptide hits" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="inAnalysis" value="" type="input-file" description="File input Analysis file .xml" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="inGlycan" value="" type="input-file" description="File input Glycan composition file .txt" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="inPeptide" value="" type="input-file" description="File input Glycopeptide file .xml" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="tolerance" value="10" type="double" description="Mass tolerance" required="false" advanced="false" /> | |
| <ITEM name="toleranceType" value="ppm" type="string" description="Type of the given mass tolerance" required="false" advanced="false" restrictions="Da,ppm" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="ConsensusSearch" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="240" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="620" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="ConsensusSearch" type="string" description="Which external tool configuration to load?! See '/afs/mpi-magdeburg.mpg.de/home/pioch/Data/software/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,FragmentationTypeFilesplitter,GlycanCompositionBuilder,GlycoDomainViewer,GlycoIdentificationScore,GlycopetideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,RAWFileConvert,PeptideFilter,QCMLExport,RAWDirConvert,RobustPeakPicker,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="inGlyML" value="" type="input-file" description="" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="outGlyML" value="" type="output-file" description="" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEM name="tolerance" value="30" type="double" description="Mass tolerance" required="false" advanced="false" /> | |
| <ITEM name="toleranceType" value="ppm" type="string" description="Type of the given mass tolerance" required="false" advanced="false" restrictions="Da,ppm" /> | |
| <ITEM name="ionthreshold" value="0" type="int" description="Threshold for reporter ion intensity to be counted for score" required="false" advanced="false" /> | |
| <ITEMLIST name="pepIons" type="string" description="Peptide ions to search for" required="false" advanced="false" restrictions="a,a-H2O,a-NH3,b,b-H2O,b-NH3,by,c,c-H2O,c-NH3,x,x-H2O,x-NH3,y,y-H2O,y-NH3,z,z-H2O,z-NH3,z*"> | |
| <LISTITEM value="b"/> | |
| <LISTITEM value="b-H2O"/> | |
| <LISTITEM value="b-NH3"/> | |
| <LISTITEM value="y"/> | |
| <LISTITEM value="y-H2O"/> | |
| <LISTITEM value="y-NH3"/> | |
| </ITEMLIST> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="GlycopeptideDigest" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="360" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="GlycopeptideDigest" type="string" description="Which external tool configuration to load?! See '/afs/mpi-magdeburg.mpg.de/home/pioch/Data/software/OpenMS/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,FragmentationTypeExtractor,FragmentationTypeFilesplitter,FragmentCheck,GlycanCompositionBuilder,GlycanScorer,GlycoDomainViewer,GlycoIdentificationScore,GlycopeptideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,glyxScore,HGIReporter,IdentificationDiscriminator,IdentificationMerger,IdentificationTransfer,RAWFileConvert,OxoniumFilter,PdfReporter,PeptideFilter,PeptideScorer,QCMLExport,RAWDirConvert,RemoveFeatures,RobustPeakPicker,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_setid,Rscript_qcfigures_tic,TPP_RefreshParser,mail,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="inFasta" value="" type="input-file" description="File input Proteinsequences, only .fasta allowed" required="false" advanced="false" supported_formats="*.fasta" /> | |
| <ITEM name="out" value="" type="output-file" description="File output peptide sequence file .xml" required="false" advanced="false" supported_formats="*.xml" /> | |
| <ITEMLIST name="enzymes" type="string" description="Digestion enzymes" required="false" advanced="false" restrictions="Trypsin,Trypsin/P,AspN,Flavastacin,ProtK,Unspecific,NoDigest"> | |
| <LISTITEM value="Trypsin"/> | |
| </ITEMLIST> | |
| <ITEM name="maxNrModifications" value="2" type="int" description="Nr of maximum allowed modifications. CYS_CAM, CYS_CM are excluded. Unlimited with -1." required="false" advanced="false" /> | |
| <ITEMLIST name="modifications" type="string" description="variable modifications" required="false" advanced="false" restrictions="None,AMID,CAM,CYS_CAM,NTERM_CAM,CM,CYS_CM,DEAM,ASN_DEAM,GLN_DEAM,DEHYDR,SER_DEHYDR,THR_DEHYDR,DIOX,TRP_DIOX,TYR_DIOX,MSO,OX,TRP_OX,TYR_OX,CYS_PAM,PHOS,SER_PHOS,THR_PHOS,TYR_PHOS,TRP_KYN"> | |
| <LISTITEM value="CYS_CAM"/> | |
| <LISTITEM value="MSO"/> | |
| </ITEMLIST> | |
| <ITEMLIST name="glycosylation" type="string" description="glycosylation" required="false" advanced="false" restrictions="N-Glycosylation,O-Glycosylation,NXC-Glycosylation,NXV-Glycosylation"> | |
| <LISTITEM value="N-Glycosylation"/> | |
| </ITEMLIST> | |
| <ITEM name="missedCleavageSites" value="2" type="int" description="maximum missed cleavage sites" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="FileFilter" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="40" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="-280" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="in" value="" type="input-file" description="Input file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="in_type" value="" type="string" description="Input file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="out" value="" type="output-file" description="Output file" required="true" advanced="false" supported_formats="*.mzML,*.featureXML,*.consensusXML" /> | |
| <ITEM name="out_type" value="" type="string" description="Output file type -- default: determined from file extension or content" required="false" advanced="false" restrictions="mzML,featureXML,consensusXML" /> | |
| <ITEM name="rt" value=":" type="string" description="Retention time range to extract" required="false" advanced="false" /> | |
| <ITEM name="mz" value=":" type="string" description="m/z range to extract (applies to ALL ms levels!)" required="false" advanced="false" /> | |
| <ITEM name="int" value=":" type="string" description="Intensity range to extract" required="false" advanced="false" /> | |
| <ITEM name="sort" value="false" type="string" description="Sorts the output according to RT and m/z." required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="peak_options" description="Peak data options"> | |
| <ITEM name="sn" value="0" type="double" description="Write peaks with S/N > 'sn' values only" required="false" advanced="false" /> | |
| <ITEMLIST name="rm_pc_charge" type="int" description="Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="pc_mz_range" value=":" type="string" description="MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag." required="false" advanced="false" /> | |
| <ITEMLIST name="pc_mz_list" type="double" description="List of m/z values. If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept." required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="level" type="int" description="MS levels to extract" required="false" advanced="false"> | |
| <LISTITEM value="1"/> | |
| <LISTITEM value="2"/> | |
| <LISTITEM value="3"/> | |
| </ITEMLIST> | |
| <ITEM name="sort_peaks" value="false" type="string" description="Sorts the peaks according to m/z" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="no_chromatograms" value="false" type="string" description="No conversion to space-saving real chromatograms, e.g. from SRM scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_chromatograms" value="false" type="string" description="Removes chromatograms stored in a file" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="mz_precision" value="64" type="string" description="Store base64 encoded m/z data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="int_precision" value="32" type="string" description="Store base64 encoded intensity data using 32 or 64 bit precision" required="false" advanced="false" restrictions="32,64" /> | |
| <ITEM name="indexed_file" value="false" type="string" description="Whether to add an index to the file when writing" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="zlib_compression" value="false" type="string" description="Whether to store data with zlib compression (lossless compression)" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="numpress" description="Numpress compression for peak data"> | |
| <ITEM name="masstime" value="none" type="string" description="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="masstime_error" value="0.0001" type="double" description="Maximal allowable error in m/z or rt dimension (default 10 ppm at 100 m/z; set to 0.5 for pic or negative to disable check and speed up conversion)" required="false" advanced="false" /> | |
| <ITEM name="intensity" value="none" type="string" description="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" required="false" advanced="false" restrictions="none,linear,pic,slof" /> | |
| <ITEM name="intensity_error" value="0.0001" type="double" description="Maximal allowable error in intensity dimension (set to 0.5 for pic or negative to disable check and speed up conversion)" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="spectra" description="Remove spectra or select spectra (removing all others) with certain properties"> | |
| <ITEM name="remove_zoom" value="false" type="string" description="Remove zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_mode" value="" type="string" description="Remove scans by scan mode" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorption" /> | |
| <ITEM name="remove_activation" value="" type="string" description="Remove MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" 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,Pulsed q dissociation" /> | |
| <ITEM name="remove_collision_energy" value=":" type="string" description="Remove MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="remove_isolation_window_width" value=":" type="string" description="Remove MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_zoom" value="false" type="string" description="Select zoom (enhanced resolution) scans" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="select_mode" value="" type="string" description="Selects scans by scan mode#br#" required="false" advanced="false" restrictions="Unknown,MassSpectrum,MS1Spectrum,MSnSpectrum,SelectedIonMonitoring,SelectedReactionMonitoring,ConsecutiveReactionMonitoring,ConstantNeutralGain,ConstantNeutralLoss,Precursor,EnhancedMultiplyCharged,TimeDelayedFragmentation,ElectromagneticRadiation,Emission,Absorption" /> | |
| <ITEM name="select_activation" value="" type="string" description="Retain MSn scans where any of its precursors features a certain activation method" required="false" advanced="false" 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,Pulsed q dissociation" /> | |
| <ITEM name="select_collision_energy" value=":" type="string" description="Select MSn scans with a collision energy in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_isolation_window_width" value=":" type="string" description="Select MSn scans whose isolation window width is in the given interval" required="false" advanced="false" /> | |
| <ITEM name="select_polarity" value="" type="string" description="Retain MSn scans with a certain scan polarity" required="false" advanced="false" restrictions="unknown,positive,negative" /> | |
| </NODE> | |
| <NODE name="feature" description="Feature data options"> | |
| <ITEM name="q" value=":" type="string" description="Overall quality range to extract [0:1]" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="consensus" description="Consensus feature data options"> | |
| <ITEMLIST name="map" type="int" description="Maps to be extracted from a consensus" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="map_and" value="false" type="string" description="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" required="false" advanced="false" restrictions="true,false" /> | |
| <NODE name="blackorwhitelist" description="Black or white listing of of MS2 spectra by consensus features"> | |
| <ITEM name="blacklist" value="true" type="string" description="True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept" required="false" advanced="false" restrictions="false,true" /> | |
| <ITEM name="file" value="" type="input-file" description="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.#br#If consensus:blackorwhitelist:maps is specified, only these will be used.#br#" required="false" advanced="false" supported_formats="*.consensusXML" /> | |
| <ITEMLIST name="maps" type="int" description="Maps used for black/white list filtering" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="rt" value="60" type="double" description="Retention tolerance [s] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.01" type="double" description="m/z tolerance [Th] for precursor to consensus feature position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="use_ppm_tolerance" value="false" type="string" description="If ppm tolerance should be used. Otherwise Da are used." required="false" advanced="false" restrictions="false,true" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="f_and_c" description="Feature & Consensus data options"> | |
| <ITEM name="charge" value=":" type="string" description="Charge range to extract" required="false" advanced="false" /> | |
| <ITEM name="size" value=":" type="string" description="Size range to extract" required="false" advanced="false" /> | |
| <ITEMLIST name="remove_meta" type="string" description="Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!" required="false" advanced="false"> | |
| </ITEMLIST> | |
| </NODE> | |
| <NODE name="id" description="ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist"> | |
| <ITEM name="remove_clashes" value="false" type="string" description="Remove features with id clashes (different sequences mapped to one feature)" required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="keep_best_score_id" value="false" type="string" description="in case of multiple peptide identifications, keep only the id with best score" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEMLIST name="sequences_whitelist" type="string" description="keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation)" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEMLIST name="accessions_whitelist" type="string" description="keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN" required="false" advanced="false"> | |
| </ITEMLIST> | |
| <ITEM name="remove_annotated_features" value="false" type="string" description="Remove features with annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unannotated_features" value="false" type="string" description="Remove features without annotations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="remove_unassigned_ids" value="false" type="string" description="Remove unassigned peptide identifications" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="blacklist" value="" type="input-file" description="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file!#br#Matching tolerances are taken from 'id:rt' and 'id:mz' options.#br#This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches." required="false" advanced="false" supported_formats="*.idXML" /> | |
| <ITEM name="rt" value="0.1" type="double" description="Retention tolerance [s] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="mz" value="0.001" type="double" description="m/z tolerance [Th] for precursor to id position" required="false" advanced="false" restrictions="0:" /> | |
| <ITEM name="blacklist_imperfect" value="false" type="string" description="Allow for mismatching precursor positions (see 'id:blacklist')" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| <NODE name="algorithm" description="S/N algorithm section"> | |
| <NODE name="SignalToNoise" description=""> | |
| <ITEM name="max_intensity" value="-1" type="int" description="maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N." required="false" advanced="true" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="double" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" required="false" advanced="true" restrictions="0:999" /> | |
| <ITEM name="auto_max_percentile" value="95" type="int" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" required="false" advanced="true" restrictions="0:100" /> | |
| <ITEM name="auto_mode" value="0" type="int" description="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" required="false" advanced="true" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="double" description="window length in Thomson" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="false" restrictions="3:" /> | |
| <ITEM name="min_required_elements" value="10" type="int" description="minimum number of elements required in a window (otherwise it is considered sparse)" required="false" advanced="false" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> | |
| <ITEM name="write_log_messages" value="true" type="string" description="Write out log messages in case of sparse windows or median in rightmost histogram bin" required="false" advanced="false" restrictions="true,false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <ITEM name="recycle_output" value="false" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_name" value="GenericWrapper" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="tool_type" value="GlycanCompositionBuilder" type="string" description="" required="false" advanced="false" /> | |
| <ITEM name="x_pos" value="-140" type="double" description="" required="false" advanced="false" /> | |
| <ITEM name="y_pos" value="560" type="double" description="" required="false" advanced="false" /> | |
| <NODE name="parameters" description=""> | |
| <ITEM name="type" value="GlycanCompositionBuilder" type="string" description="Which external tool configuration to load?! See 'C:/Program Files/OpenMS-2.3.0/share/OpenMS/TOOLS/EXTERNAL'." required="false" advanced="false" restrictions="ConsensusSearch,glyxFeatureExtractor,FeatureFinderMS,FileBuilder,FragmentationTypeExtractor,FragmentationTypeFilesplitter,FragmentCheck,GlycanCompositionBuilder,GlycanScorer,GlycoDomainViewer,GlycoIdentificationScore,GlycopeptideDigest,GlycopeptideMatcher,GlycopeptideTable,glyxFilter,glyxReporter,hardklor,HexNAcRatio,HGIReporter,IdentificationDiscriminator,IdentificationMerger,IdentificationTransfer,MascotPercolator,RAWFileConvert,MSGFtoPercolator,OxoniumFilter,PdfReporter,PeptideFilter,PeptideScorer,Percolator,QCMLExport,RAWDirConvert,RemoveFeatures,RobustPeakPicker,Rscript_generic,Rscript_mzTab2tsv_PEP,Rscript_mzTab2tsv_PRT,Rscript_mzTab2tsv_PSM,Rscript_qcfigures_acc,Rscript_qcfigures_idmap,Rscript_qcfigures_rt_acc,Rscript_qcfigures_setid,Rscript_qcfigures_tic,Rscript_qcfigures_inj,TPP_RefreshParser,XTandemToPercolator,TPP_ProteinProphet" /> | |
| <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> | |
| <ITEM name="no_progress" value="true" type="string" description="Disables progress logging to command line" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" /> | |
| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" /> | |
| <NODE name="ETool" description="tool specific parameters"> | |
| <ITEM name="scriptpath" value="C:/Program Files/OpenMS-2.3.0\share/OpenMS/SCRIPTS" type="string" description="input script path, this should point to share/OpenMS/SCRIPTS of your OpenMS installation" required="false" advanced="false" /> | |
| <ITEM name="in" value="" type="input-file" description="input file if glycan compositions should be filtered" required="false" advanced="false" /> | |
| <ITEM name="out" value="" type="output-file" description="File output glycan composition file .txt" required="false" advanced="false" supported_formats="*.txt" /> | |
| <ITEM name="useAsFilter" value="true" type="string" description="Use as filter of glycan compositions from input file, otherwise use glycan ranges to calculate all permutations" required="false" advanced="false" restrictions="true,false" /> | |
| <ITEM name="rangeHex" value="3:16" type="string" description="Range of Hex within the glycan, use min:max as input" required="false" advanced="false" /> | |
| <ITEM name="rangeHexNAc" value="2:14" type="string" description="Range of HexNAc within the glycan, use min:max as input" required="false" advanced="false" /> | |
| <ITEM name="rangeFuc" value="0:6" type="string" description="Range of Fucose within the glycan, use min:max as input" required="false" advanced="false" /> | |
| <ITEM name="rangeNeuAc" value="0:5" type="string" description="Range of NeuAc within the glycan, use min:max as input" required="false" advanced="false" /> | |
| <ITEM name="rangeNeuGc" value="0:3" type="string" description="Range of NeuAc within the glycan, use min:max as input" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| <NODE name="edges" description=""> | |
| <NODE name="0" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="6/7" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inReplace" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="1" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/8" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="2" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="6/9" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inMZML" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="3" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/13" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:outFeature" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="4" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="7/10" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inMZML" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="5" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="9/10" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:outFeature" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inFeature" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="6" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="10/11" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:outGlyML" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inAnalysis" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="7" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="11/12" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inGlyML" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="8" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="12/14" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:outGlyML" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="9" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="1/3" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inFasta" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="10" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="3/11" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inPeptide" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="11" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="0/4" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="12" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/6" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="13" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="4/7" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inOriginal" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="14" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="2/5" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="__no_name__" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:in" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| <NODE name="15" description=""> | |
| <NODE name="source/target" description=""> | |
| <ITEM name="" value="5/11" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="source_out_param" description=""> | |
| <ITEM name="" value="ETool:out" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| <NODE name="target_in_param" description=""> | |
| <ITEM name="" value="ETool:inGlycan" type="string" description="" required="false" advanced="false" /> | |
| </NODE> | |
| </NODE> | |
| </NODE> | |
| </PARAMETERS> |
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