Update parameters in README

README.md

@@ -54,14 +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
- 	--organism 		 Input organism [hg38 | hg19 | mm9 | mm10]
+	--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.
-	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will be skipped.
+	--tfbs_path 		Path to directory with tfbsscan output. If given tfbsscan will be skipped.
 
 	Footprint extraction:
 	--window_length INT	This parameter sets the length of a sliding window. (Default: 200)
@@ -78,7 +78,7 @@ Optional arguments:
 	Sequence preparation/ reduction:
 	--kmer INT		K-mer length (Default: 10)
 	--aprox_motif_len INT	Motif length (Default: 10)
-	--motif_occurence FLOAT	Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
+	--motif_occurrence FLOAT	Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif.
 	--min_seq_length Interations	Remove all sequences below this value. (Default: 10)
 	Clustering:
 	--global INT		Global (=1) or local (=0) alignment. (Default: 0)
@@ -96,14 +96,17 @@ Optional arguments:
 	--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)
+	--seed Set seed for GLAM2 (Default: 123456789)
 	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)
 
 	Creating GTF:
 	--tissues List/String 	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON
 				config
+	Evaluation:
+	--max_uropa_runs INT	 Maximum number UROPA runs running parallelized (Default: 10)
 All arguments can be set in the configuration files
  ```