Mercurial > repos > galaxyp > cardinal_preprocessing

comparison preprocessing.xml @ 12:e0669b1854b1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8"
author galaxyp
date Thu, 22 Oct 2020 20:38:29 +0000
parents e86a8be551b9
children 6b36be80febb
comparison
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11:e86a8be551b9 12:e0669b1854b1
834 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed after the data is read by the tool. 834 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed after the data is read by the tool.
835 @MZ_TABULAR_INPUT_DESCRIPTION@ 835 @MZ_TABULAR_INPUT_DESCRIPTION@
836 836
837 **Options** 837 **Options**
838 838
839 - Normalization: Normalization of intensities to total ion current (TIC) or to root-mean-square (RMS) 839 - Normalization: normalization of intensities to total ion current (TIC) or to root-mean-square (RMS)
840 - Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets) 840 - Baseline reduction: baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets)
841 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection 841 - Smoothing: Smoothing of the peaks reduces noise and improves peak detection
842 - m/z alignment: removes small m/z shifts between spectra
842 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards) 843 - Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
843 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept 844 - Peak alignment: only possible after peak picking, m/z inaccuracies are removed by alignment of same peaks to a common m/z value; if no reference is given the peaks are aligned to the local maxima of the mean spectrum of the current dataset; external reference data can be used from another MSI data file or a tabular file with m/z values, but then only the m/z from the reference will be kept
844 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot 845 - Peak filtering: removes peaks that occur only in a small proportion of pixels. If not sure which cut off to choose run quality control tool first and decide according to the number of peaks per m/z plot
845 - Peak binning: extracts peaks intensities (from a profile dataset) for a list of m/z (reference) values 846 - Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
846 - Data reduction: binning or resampling to reduce data 847 - m/z binning: generates new m/z bins
847 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 848 - Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems.
849
848 850
849 **Output** 851 **Output**
850 852
851 - MSI data as continuous or processed imzML file 853 - MSI data as continuous or processed imzML file
852 - pdf with key values and four random mass spectra after each processing step 854 - pdf with key values and four random mass spectra after each processing step