Update: new parameters

README.md

@@ -54,13 +54,14 @@ Required arguments:
 	--genome_fasta		 Path to genome in FASTA-format
 	--motif_db		 Path to motif-database in MEME-format
 	--config		 Path to UROPA configuration file
+	--gtf_annotation	Path to gtf annotation file
 	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
 	--out			 Output Directory (Default: './out/')
 
 Optional arguments:
 
 	--help [0|1]		1 to show this help message. (Default: 0)
-	--gtf_path		Path to gtf-file. If path is set the process which creates a gtf-file is skipped.
+	--gtf_merged		Path to gtf-file. If path is set the process which creates a gtf-file is skipped.
 	--tfbs_path 		Path to directory with tfbsscan output. If given tfbsscan will be skipped.
 
 	Footprint extraction: