README: parameter update

README.md

@@ -62,14 +62,17 @@ Required arguments:
 	--config		 Path to UROPA configuration file
  	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
 	--out			 Output Directory (Default: './out/')
+	[
+	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
+				 Path can be set as tfbs_path in next run. (Needs absolute path)
+	or
+	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run. (Needs absolute path)
+	]
 
 Optional arguments:
 
 	--help [0|1]		1 to show this help message. (Default: 0)
-	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will not be run.
-	--create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored.
-				 Path can be set as tfbs_path in next run. (Default: './')
-	--gtf_path			Path to gtf-file. If path is set the process which creats a gtf-file is skipped.
+	--gtf_path		Path to gtf-file. If path is set the process which creats a gtf-file is skipped.
 
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
@@ -103,8 +106,9 @@ Optional arguments:
 	--iteration INT		Number of iterations done by GLAM2. More Iterations: better results, higher runtime. (Default: 10000)
 	--tomtom_treshold FLOAT	Threshold for similarity score. (Default: 0.01)
 	--best_motif INT	Get the best X motifs per cluster. (Default: 3)
+	--gap_penalty INT	Set penalty for gaps in GLAM2 (Default: 1000)
 	Moitf clustering:
-	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Default: 0)
+	--cluster_motif	Boolean	If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0)
 	--edge_weight INT	Minimum weight of edges in motif-cluster-graph (Default: 5)
 	--motif_similarity_thresh FLOAT	Threshold for motif similarity score (Default: 0.00001)