README.md in bio-gemma-wrapper-0.97.1 vs README.md in bio-gemma-wrapper-0.98

@@ -1,5 +1,7 @@
+[![Gem Version](https://badge.fury.io/rb/bio-gemma-wrapper.svg)](https://badge.fury.io/rb/bio-gemma-wrapper)
+
 # GEMMA wrapper caches K between runs with LOCO support
 
 ![Genetic associations identified in CFW mice using GEMMA (Parker et al,
 Nat. Genet., 2016)](cfw.gif)
 
@@ -37,14 +39,16 @@
 
 Invoke the tool with
 
     gemma-wrapper --help
 
-and it will render
+and it will render something like
 
 ```
 Usage: gemma-wrapper [options] -- [gemma-options]
+        --permutate n                Permutate # times by shuffling phenotypes
+        --permute-phenotypes filen   Phenotypes to be shuffled in permutations
         --loco [x,y,1,2,3...]        Run full LOCO
         --input filen                JSON input variables (used for LOCO)
         --cache-dir path             Use a cache directory
         --json                       Create output file in JSON format
         --force                      Force computation
@@ -93,10 +97,11 @@
 
     /tmp/3079151e14b219c3b243b673d88001c1675168b4.log.txt gemma-wrapper CACHE HIT!
 
 gemma-wrapper computes the unique HASH value over the command
 line switches passed into GEMMA as well as the contents of the files
-passed in (here the genotype and phenotype files).
+passed in (here the genotype and phenotype files - actually it ignores the phenotype with K because
+GEMMA always computes the same K).
 
 You can also get JSON output on STDOUT by providing the --json switch
 
     gemma-wrapper --json -- \
         -g test/data/input/BXD_geno.txt.gz \