Input files to align (all must have the same file type) [mzML,featureXML]File to use as reference (same file format as input files required) [mzML,featureXML,opt.]Output files (same file type as 'in'). Either this option or 'trafo_out' has to be provided; they can be used together. [mzML,featureXML,Inactive]Transformation output files. Either this option or 'out' has to be provided; they can be used together. [trafoXML,Inactive]The text sent to standard out during the execution of MapAlignerPoseClustering.The text sent to standard error during the execution of MapAlignerPoseClustering. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)