def execute(cls, choices, galaxyFn=None, username=''): inGSuite = getGSuiteFromGalaxyTN(choices.gsuite) if choices.genome != inGSuite.genome: inGSuite.setGenomeOfAllTracks(choices.genome) registerGSuiteTrackClass(FileGSuiteTrack) outGSuite = GSuite() for track in inGSuite.allTracks(): origGalaxyTN = ETM.createGalaxyTnFromExternalTn(track.trackName) uri = FileGSuiteTrack.generateURI( path=ETM.extractFnFromGalaxyTN(origGalaxyTN), suffix=ETM.extractFileSuffixFromGalaxyTN(origGalaxyTN)) newTrack = GSuiteTrack(uri, title=track.title, trackType=track.trackType, genome=track.genome, attributes=track.attributes) outGSuite.addTrack(newTrack) GSuiteComposer.composeToFile(outGSuite, galaxyFn)