Available Fragment Commands

To get a list of available commands, you can query maltcms directly:

>maltcms.sh -l cross.commands.fragments.AFragmentCommand

To find out about the parameters supported by an individual command:

>maltcms.sh -s maltcms.commands.fragments.peakfinding.TICPeakFinder

If you want to generate a basic configuration file for a number of commands:

>maltcms.sh -b maltcms.commands.fragments.peakfinding.TICPeakFinder

You can provide multiple commands by separating them with a ','. The created pipeline will be in the 'maltcmsOutput/pipelines/' directory below the current working directory. The created files are just a starting point and will most probably not work immediately. For hints on completing the configuration files, please consult the provided pipelines below 'cfg/pipelines/' and 'cfg/pipelines/xml'.

If you have further questions, please feel free to contact the author.

List of Fragment Commands

Currently, the following fragment commands are available for execution within the pipeline. Other fragment commands may be available, but have not yet been finalized for description in this file.

maltcms.commands.fragments.preprocessing.

  • TICPeakFinder : Finds well conserved peaks in the TIC
  • DenseArrayProducer : produces evenly binned intensity profiles
  • DefaultVarLoader : loads default variables

maltcms.commands.fragments.io.

  • ANDIChromImporter : import for AIA/AndiChrom files
  • ANDIMSExporter : export to AIA/ANDIMS files
  • CSVAnchorReader : read anchors in csv format
  • ObiWarplmataExporter : export profile matrices to ObiWarp's lmata format
  • VariableDataExporter : exports selected variables to csv files

maltcms.commands.fragments.cluster.

  • PairwiseDistanceCalculator : calculates pairwise distances/similarities between chromatograms
  • CompleteLinkageAlgorithm : applies CompleteLinkage based on pairwise distances
  • NeighborJoinAlgorithm : applies NeighborJoining
  • SingleLinkageAlgorithm : applies SingleLinkage
  • UPGMAAlgorithm : applies UPGMA (AverageLinkage)

maltcms.commands.fragments.assignment.

  • PeakCliqueAssignment : assigns peaks to cliques based on ms similarity, rt deviation and a bidirectional best hits criterion
  • EIMSMDBetaboliteAssignment : assigns peaks with possibly multiple matches against a MetaboliteDB instance with cosine score criterion

maltcms.commands.fragments.alignment.

  • CenterStarAlignment : selects the chromatogram with smallest overall distance to other chroms as alignment reference
  • ProgressiveTreeAlignment : generates a consensus, time corrected chromatogram as alignment reference

maltcms.commands.fragments.visualization.

  • Array1DVisualizer : visualize 1D data, e.g. TICs
  • ChromatogramVisualizer : visualize chromatograms as heatmaps
  • MZIDistributionVisualizer : visualize distribution of m/z values as histogram
  • PairwiseAlignmentMatrixVisualizer : visualize pairwise alignment matrix
  • PairwiseAlignmentVisualizer : visualize pairwise alignments
  • ScoreDistributionVisualizer : visualize score distribution histogram

maltcms.commands.fragments2d.preprocessing

  • Data2DNormalizer : normalization and filtering of 2D TIC data
  • ModulationExtractor : extracts slices of 2D GCxGC-MS data
  • GCGCToGCMSConverter : resamples 2D GCxGC-MS data to GC-MS data by integrating modulations

maltcms.commands.fragments2d.visualization

  • Chromatogram2DVisualizer : 2D heatmap visualization of 2D TIC data

maltcms.commands.fragments2d.warp

  • Variants of Dynamic Time Warping for alignment of 2D TIC data

maltcms.commands.fragments2d.warp.visualization

  • Visualizations for Dynamic Time Warping alignments of 2D TIC data

maltcms.commands.fragments2d.peakfinding

  • SeededRegionGrowing : locates and integrates 2D-TIC peaks in GCxGC-MS data, performs putative database identification and multiple peak alignment