Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
view test-data/examples/TOPPAS/peakpicker_tutorial.toppas @ 18:6daaa75ccb99 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
| author | galaxyp |
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| date | Sun, 13 Dec 2020 15:03:50 +0000 |
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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="1.11.0" type="string" description="" required="false" advanced="false" /> <ITEM name="num_vertices" value="5" type="int" description="" required="false" advanced="false" /> <ITEM name="num_edges" value="4" type="int" description="" required="false" advanced="false" /> <ITEM name="description" value="<![CDATA[<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Arial'; font-size:12pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Basic peak picking pipeline using PeakPickerWavelet (use PeakPickerHiRes instead if you have high-resolution data as it is much faster).</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Using NoiseFilterSGolay (assuming low-res data) and BaselineFilter (for MALDI data).</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; color:#000000;"></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" color:#000000;">Depending on your data, either of the two filters may be removed or reconfigured with other parameters.</span></p></body></html>]]>" 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="../peakpicker_tutorial_1.mzML"/> </ITEMLIST> <ITEM name="x_pos" value="-320" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="0" 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="tool" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_name" value="NoiseFilterSGolay" 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="0" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEM name="in" value="" type="input-file" description="input raw data file " required="true" advanced="false" supported_formats="*.mzML" /> <ITEM name="out" value="" type="output-file" description="output raw data file " required="true" advanced="false" supported_formats="*.mzML" /> <ITEM name="log" value="TOPP.log" 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="algorithm" description="Algorithm parameters section"> <ITEM name="frame_length" value="11" type="int" description="The number of subsequent data points used for smoothing.#br#This number has to be uneven. If it is not, 1 will be added." required="false" advanced="false" /> <ITEM name="polynomial_order" value="3" type="int" description="Order or the polynomial that is fitted." required="false" advanced="false" /> </NODE> </NODE> </NODE> <NODE name="2" 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="BaselineFilter" 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="0" type="double" description="" required="false" advanced="false" /> <NODE name="parameters" description=""> <ITEM name="in" value="" type="input-file" description="input raw data file " required="true" advanced="false" supported_formats="*.mzML" /> <ITEM name="out" value="" type="output-file" description="output raw data file " required="true" advanced="false" supported_formats="*.mzML" /> <ITEM name="struc_elem_length" value="3" type="double" description="Length of the structuring element (should be wider than maximal peak width - see documentation)." required="false" advanced="false" /> <ITEM name="struc_elem_unit" value="Thomson" type="string" description="Unit of 'struc_elem_length' parameter." required="false" advanced="false" restrictions="Thomson,DataPoints" /> <ITEM name="method" value="tophat" type="string" description="The name of the morphological filter to be applied. If you are unsure, use the default." required="false" advanced="false" restrictions="identity,erosion,dilation,opening,closing,gradient,tophat,bothat,erosion_simple,dilation_simple" /> <ITEM name="log" value="TOPP.log" 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> </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="PeakPickerWavelet" type="string" description="" required="false" advanced="false" /> <ITEM name="tool_type" value="" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="220" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="0" 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="write_peak_meta_data" value="false" type="string" description="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file.Attention: this can blow up files,as 7 arrays are stored per spectrum!" required="false" advanced="true" restrictions="true,false" /> <ITEM name="log" value="TOPP.log" 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="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." required="false" advanced="false" restrictions="0:" /> <ITEM name="centroid_percentage" value="0.8" type="double" description="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid. If it is 1 the centroid position corresponds to the position of the highest intensity." required="false" advanced="true" restrictions="0:1" /> <ITEM name="peak_width" value="0.15" type="double" description="Approximate fwhm of the peaks." required="false" advanced="false" restrictions="0:" /> <ITEM name="estimate_peak_width" value="false" type="string" description="Flag if the average peak width shall be estimated. Attention: when this flag is set, the peak_width is ignored." required="false" advanced="false" restrictions="true,false" /> <ITEM name="fwhm_lower_bound_factor" value="0.7" type="double" description="Factor that calculates the minimal fwhm value from the peak_width. All peaks with width smaller than fwhm_bound_factor * peak_width are discarded." required="false" advanced="true" restrictions="0:" /> <ITEM name="fwhm_upper_bound_factor" value="20" type="double" description="Factor that calculates the maximal fwhm value from the peak_width. All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded." required="false" advanced="true" restrictions="0:" /> <ITEM name="optimization" value="no" type="string" description="If the peak parameters position, intensity and left/right widthshall be optimized set optimization to one_dimensional or two_dimensional." required="false" advanced="true" restrictions="no,one_dimensional,two_dimensional" /> <NODE name="thresholds" description=""> <ITEM name="peak_bound" value="10" type="double" description="Minimal peak intensity." required="false" advanced="true" restrictions="0:" /> <ITEM name="peak_bound_ms2_level" value="10" type="double" description="Minimal peak intensity for MS/MS peaks." required="false" advanced="true" restrictions="0:" /> <ITEM name="correlation" value="0.5" type="double" description="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." required="false" advanced="true" restrictions="0:1" /> <ITEM name="noise_level" value="0.1" type="double" description="noise level for the search of the peak endpoints." required="false" advanced="true" restrictions="0:" /> <ITEM name="search_radius" value="3" type="int" description="search radius for the search of the maximum in the signal after a maximum in the cwt was found" required="false" advanced="true" restrictions="0:" /> </NODE> <NODE name="wavelet_transform" description=""> <ITEM name="spacing" value="0.001" type="double" description="spacing of the cwt." required="false" advanced="true" restrictions="0:" /> </NODE> <NODE name="optimization" description=""> <ITEM name="iterations" value="15" type="int" description="maximal number of iterations for the fitting step" required="false" advanced="true" restrictions="1:" /> <NODE name="penalties" description=""> <ITEM name="position" value="0" type="double" description="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " required="false" advanced="true" restrictions="0:" /> <ITEM name="left_width" value="1" type="double" description="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> <ITEM name="right_width" value="1" type="double" description="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> <ITEM name="height" value="1" type="double" description="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> </NODE> <NODE name="2d" description=""> <ITEM name="tolerance_mz" value="2.2" type="double" description="mz tolerance for cluster construction" required="false" advanced="true" restrictions="0:" /> <ITEM name="max_peak_distance" value="1.2" type="double" description="maximal peak distance in mz in a cluster" required="false" advanced="true" restrictions="0:" /> </NODE> </NODE> <NODE name="deconvolution" description=""> <ITEM name="deconvolution" value="false" type="string" description="If you want heavily overlapping peaks to be separated set this value to "true"" required="false" advanced="true" restrictions="true,false" /> <ITEM name="asym_threshold" value="0.3" type="double" description="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started." required="false" advanced="true" restrictions="0:" /> <ITEM name="left_width" value="2" type="double" description="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." required="false" advanced="true" restrictions="0:" /> <ITEM name="right_width" value="2" type="double" description="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." required="false" advanced="true" restrictions="0:" /> <ITEM name="scaling" value="0.12" type="double" description="Initial scaling of the cwt used in the seperation of heavily overlapping peaks. The initial value is used for charge 1, for higher charges it is adapted to scaling/charge." required="false" advanced="true" restrictions="0:" /> <NODE name="fitting" description=""> <ITEM name="fwhm_threshold" value="0.7" type="double" description="If the fwhm of a peak is higher than fwhm_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started." required="false" advanced="true" restrictions="0:" /> <ITEM name="eps_abs" value="9.99999974737875e-006" type="double" description="if the absolute error gets smaller than this value the fitting is stopped." required="false" advanced="true" restrictions="0:" /> <ITEM name="eps_rel" value="9.99999974737875e-006" type="double" description="if the relative error gets smaller than this value the fitting is stopped." required="false" advanced="true" restrictions="0:" /> <ITEM name="max_iteration" value="10" type="int" description="maximal number of iterations for the fitting step" required="false" advanced="true" restrictions="1:" /> <NODE name="penalties" description=""> <ITEM name="position" value="0" type="double" description="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule." required="false" advanced="true" restrictions="0:" /> <ITEM name="height" value="1" type="double" description="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> <ITEM name="left_width" value="0" type="double" description="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> <ITEM name="right_width" value="0" type="double" description="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized." required="false" advanced="true" restrictions="0:" /> </NODE> </NODE> </NODE> <NODE name="SignalToNoiseEstimationParameter" 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 not be added to the histogram. 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)." 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="true" restrictions="1:" /> <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" required="false" advanced="true" restrictions="3:" /> <ITEM name="stdev_mp" value="3" type="double" description="multiplier for stdev" required="false" advanced="true" restrictions="0.01:999" /> <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="true" restrictions="1:" /> <ITEM name="noise_for_empty_window" value="1e+020" type="double" description="noise value used for sparse windows" required="false" advanced="true" /> </NODE> </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="output file list" type="string" description="" required="false" advanced="false" /> <ITEM name="x_pos" value="400" type="double" description="" required="false" advanced="false" /> <ITEM name="y_pos" value="0" type="double" description="" required="false" advanced="false" /> </NODE> </NODE> <NODE name="edges" description=""> <NODE name="0" description=""> <NODE name="source/target" description=""> <ITEM name="" value="0/1" 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="1" description=""> <NODE name="source/target" description=""> <ITEM name="" value="1/2" 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="2" description=""> <NODE name="source/target" description=""> <ITEM name="" value="2/3" 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="3" description=""> <NODE name="source/target" description=""> <ITEM name="" value="3/4" 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="__no_name__" type="string" description="" required="false" advanced="false" /> </NODE> </NODE> </NODE> </PARAMETERS>