YAY

Author: ellistorrance

README.md

@@ -145,38 +145,28 @@ conda activate Tiger
 ### Islander Requirements:
  The only requirment of Islander is an output directory containing a single genomic file in fasta format with a '.fa' subscript.
 
-*Islander Flags*
  ***
-  '-outDir':    Output directory. Default: same directory as GENOME_FASTA_FILE.
-
-  '-tax':       Taxonomic info for query genome. Enter file in outDir containing 
+ *Islander Flags:*
+ - '-outDir':    Output directory. Default: same directory as GENOME_FASTA_FILE.
+ - '-tax':       Taxonomic info for query genome. Enter file in outDir containing 
                NCBI taxonomy string with a '.tax' subscript, or use B for Bacteria, 
                A for Archaea, M for Mycoplasmatales/Entomoplasmatales, G for 
                Gracilibacteria/candidate division SR1. Automatically sets -gencode. 
                Default: B.
-
-  '-gencode':   Genetic code table (see NCBI). Default: 11
-
-  '-nickname':  Brief name for genome (as might be used to start a locus_tag).
-
-  '-criterion': Basis for overlap resolution, 3 options: random, score (7-test
+ - '-gencode':   Genetic code table (see NCBI). Default: 11
+ - '-nickname':  Brief name for genome (as might be used to start a locus_tag).
+ - '-criterion': Basis for overlap resolution, 3 options: random, score (7-test
                false positive formula), deltaGC. Default = score.
-
-  '-virus':     Comma-separated list of entries assigned as viruses.
-
-  '-complete':  Consider genome complete and categorize replicons. Default:
+ - '-virus':     Comma-separated list of entries assigned as viruses.
+ - '-complete':  Consider genome complete and categorize replicons. Default:
                 consider genome incomplete and call all entries contigs.
-  '-force':     Overwrite current output files. Default: leave existing files.
-
-  '-cpu':       Number of cpus to use. Default: $cpu.
-
-  '-tateronly': Toggle to exit after running tater.pl annotator. Default: off.
-
-  Additional options: '-help', '-version', '-verbose', '-authors', '-license'
-
+ - '-force':     Overwrite current output files. Default: leave existing files.
+ - '-cpu':       Number of cpus to use. Default: $cpu.
+ - '-tateronly': Toggle to exit after running tater.pl annotator. Default: off.
+ - Additional options: '-help', '-version', '-verbose', '-authors', '-license'
 ***
 
-Example:
+Executing Islander Example:
 
 From your Conda Environment:
 ```bash