comparison preprocessing.xml @ 12:e0669b1854b1 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ca7bdf2cbc8a79278c56ab6890e038710a2a9ad8"

11:e86a8be551b9

- 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.
@MZ_TABULAR_INPUT_DESCRIPTION@

**Options**

- Normalization: Normalization of intensities to total ion current (TIC) or to root-mean-square (RMS)
- Baseline reduction: Baseline  reduction removes background intensity generated by chemical noise (common in MALDI datasets)
- Smoothing: Smoothing of the peaks reduces noise and improves peak detection
- Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
- 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
- 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
- Peak binning: extracts peaks intensities (from a profile dataset) for a list of m/z (reference) values
- Data reduction: binning or resampling to reduce data
- Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 

**Output**

- MSI data as continuous or processed imzML file
- pdf with key values and four random mass spectra after each processing step

12:e0669b1854b1

- 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.
@MZ_TABULAR_INPUT_DESCRIPTION@

**Options**

- Normalization: normalization of intensities to total ion current (TIC) or to root-mean-square (RMS)
- Baseline reduction: baseline  reduction removes background intensity generated by chemical noise (common in MALDI datasets)
- Smoothing: Smoothing of the peaks reduces noise and improves peak detection
- m/z alignment: removes small m/z shifts between spectra 
- Peak picking: relevant peaks are picked while noise-peaks are removed (needs peak alignment afterwards)
- 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
- 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
- Peak binning: extracts peaks intensities, either peak height or area under curve (from a profile dataset) for a list of m/z (reference) values
- m/z binning: generates new m/z bins
- Transformation: log2 or squareroot transformation of all intensities; when using log2 transformation zero intensities will become NA, this can lead to compatibility problems. 
                    

**Output**

- MSI data as continuous or processed imzML file
- pdf with key values and four random mass spectra after each processing step