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June 8, 2016 13:04
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| <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> | |
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| <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> | |
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| <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="" /> | |
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| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
| <ITEM name="toppas_type" value="tool" type="string" description="" /> | |
| <ITEM name="tool_name" value="NoiseFilterSGolay" type="string" description="" /> | |
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| <ITEM name="in" value="" type="string" description="input raw data file " tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output raw data file " tags="output file,required" restrictions="*.mzML" /> | |
| <ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" /> | |
| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
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| <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" 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." /> | |
| <ITEM name="polynomial_order" value="3" type="int" description="Order or the polynomial that is fitted." /> | |
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| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
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| <ITEM name="struc_elem_length" value="3" type="float" description="Length of the structuring element (should be wider than maximal peak width - see documentation)." /> | |
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| <ITEM name="method" value="tophat" type="string" description="The name of the morphological filter to be applied. If you are unsure, use the default." restrictions="identity,erosion,dilation,opening,closing,gradient,tophat,bothat,erosion_simple,dilation_simple" /> | |
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| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
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| <ITEM name="recycle_output" value="false" type="string" description="" /> | |
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| <ITEM name="tool_name" value="PeakPickerWavelet" type="string" description="" /> | |
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| <ITEM name="in" value="" type="string" description="input profile data file " tags="input file,required" restrictions="*.mzML" /> | |
| <ITEM name="out" value="" type="string" description="output peak file " tags="output file,required" restrictions="*.mzML" /> | |
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| <ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" /> | |
| <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" /> | |
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| <ITEM name="signal_to_noise" value="1" type="float" description="Minimal signal to noise ratio for a peak to be picked." restrictions="0:" /> | |
| <ITEM name="centroid_percentage" value="0.8" type="float" 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." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="peak_width" value="0.15" type="float" description="Approximate fwhm of the peaks." 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." restrictions="true,false" /> | |
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| <ITEM name="fwhm_upper_bound_factor" value="20" type="float" 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." tags="advanced" 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." tags="advanced" restrictions="no,one_dimensional,two_dimensional" /> | |
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| <ITEM name="peak_bound" value="10" type="float" description="Minimal peak intensity." tags="advanced" restrictions="0:" /> | |
| <ITEM name="peak_bound_ms2_level" value="10" type="float" description="Minimal peak intensity for MS/MS peaks." tags="advanced" restrictions="0:" /> | |
| <ITEM name="correlation" value="0.5" type="float" description="minimal correlation of a peak and the raw signal. If a peak has a lower correlation it is skipped." tags="advanced" restrictions="0:1" /> | |
| <ITEM name="noise_level" value="0.1" type="float" description="noise level for the search of the peak endpoints." tags="advanced" 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" tags="advanced" restrictions="0:" /> | |
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| <NODE name="wavelet_transform" description=""> | |
| <ITEM name="spacing" value="0.001" type="float" description="spacing of the cwt." tags="advanced" restrictions="0:" /> | |
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| <NODE name="optimization" description=""> | |
| <ITEM name="iterations" value="15" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" /> | |
| <ITEM name="delta_abs_error" value="9.99999974737875e-05" type="float" description="if the absolute error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" /> | |
| <ITEM name="delta_rel_error" value="9.99999974737875e-05" type="float" description="if the relative error gets smaller than this value the fitting is stopped" tags="advanced" restrictions="0:" /> | |
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| <ITEM name="position" value="0" type="float" description="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized " tags="advanced" restrictions="0:" /> | |
| <ITEM name="left_width" value="1" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="right_width" value="1" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="height" value="1" type="float" 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." tags="advanced" restrictions="0:" /> | |
| </NODE> | |
| <NODE name="2d" description=""> | |
| <ITEM name="tolerance_mz" value="2.2" type="float" description="mz tolerance for cluster construction" tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_peak_distance" value="1.2" type="float" description="maximal peak distance in mz in a cluster" tags="advanced" 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"" tags="advanced" restrictions="true,false" /> | |
| <ITEM name="asym_threshold" value="0.3" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="left_width" value="2" type="float" description="1/left_width is the initial value for the left width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" /> | |
| <ITEM name="right_width" value="2" type="float" description="1/right_width is the initial value for the right width of the peaks found in the deconvolution step." tags="advanced" restrictions="0:" /> | |
| <ITEM name="scaling" value="0.12" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <NODE name="fitting" description=""> | |
| <ITEM name="fwhm_threshold" value="0.7" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="eps_abs" value="9.99999974737875e-06" type="float" description="if the absolute error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" /> | |
| <ITEM name="eps_rel" value="9.99999974737875e-06" type="float" description="if the relative error gets smaller than this value the fitting is stopped." tags="advanced" restrictions="0:" /> | |
| <ITEM name="max_iteration" value="10" type="int" description="maximal number of iterations for the fitting step" tags="advanced" restrictions="1:" /> | |
| <NODE name="penalties" description=""> | |
| <ITEM name="position" value="0" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="height" value="1" type="float" description="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized." tags="advanced" restrictions="0:" /> | |
| <ITEM name="left_width" value="0" type="float" 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." tags="advanced" restrictions="0:" /> | |
| <ITEM name="right_width" value="0" type="float" 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." tags="advanced" 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)." tags="advanced" restrictions="-1:" /> | |
| <ITEM name="auto_max_stdev_factor" value="3" type="float" description="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" tags="advanced" 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" tags="advanced" 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" tags="advanced" restrictions="-1:1" /> | |
| <ITEM name="win_len" value="200" type="float" description="window length in Thomson" tags="advanced" restrictions="1:" /> | |
| <ITEM name="bin_count" value="30" type="int" description="number of bins for intensity values" tags="advanced" restrictions="3:" /> | |
| <ITEM name="stdev_mp" value="3" type="float" description="multiplier for stdev" tags="advanced" 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)" tags="advanced" restrictions="1:" /> | |
| <ITEM name="noise_for_empty_window" value="1e+20" type="float" description="noise value used for sparse windows" tags="advanced" /> | |
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from old website's workflow section:
�Basic peak picking pipeline using PeakPickerWavelet (use PeakPickerHiRes instead if you have high-resolution data as it is much faster).
Using NoiseFilterSGolay (assuming low-res data) and BaselineFilter (for MALDI data).
Depending on your data, either of the two filters may be removed or reconfigured with other parameters.