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The Flux Capacitor provides a wrapper script to launch the program from predominant shell interpreters of major platforms. |
shell (Linux/Unix) |
| cmd (Windows) |
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When started without parameters, the Flux Capacitor provides a list of command line flags that can be provided when starting the program. |
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Flux-Capacitor v1.0.3-SNAPSHOT (Flux Library: 1.15-SNAPSHOT) [ERROR] [ERROR] No parameter file specified! [ERROR] The Flux Capacitor Tool specific options [(-p|--parameter) <file>] specify parameter file (PAR file) [(-a|--annotation) <gtf>] Path to the annotation file [(-i|--input) <bed>] Path to the mapping file [(-o|--output) <gtf>] Path to the output file [(-m|--annotation-mapping) <mapping>] Annotation Mapping (default PAIRED) (default: PAIRED) [(-d|--read-descriptor) <descriptor>] Read Descriptor (default PAIRED) (default: PAIRED) [-r|--sort-in-ram] Sort in RAM [--printParameters] Print default parameters |
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As can be seen by the default output above, the Flux Capacitor requires a parameter file to be specified by the command line flag " |
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$ flux-capacitor --printParameters Flux-Capacitor v1.0.3-SNAPSHOT (Flux Library: 1.15-SNAPSHOT) # The annotation file # ANNOTATION_FILE # Information from the read descriptor that will be used for annotation mapping # # [PAIRED, STRANDED, SINGLE, COMBINED] default: SINGLE ANNOTATION_MAPPING SINGLE #... |
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A complete description of the parameters for the Flux Capacitor can be found here. |