readme stuff

Author: ellistorrance

README.md

@@ -145,26 +145,37 @@ 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.
 
-  -outDir:    Output directory. Default: same directory as GENOME_FASTA_FILE.
-  -tax:       Taxonomic info for query genome. Enter file in outDir containing 
+  **-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:
+
 From your Conda Environment:
 ```bash
 conda activate Tiger