Fixerd readme type and updated argument spacing.

README.md

@@ -15,21 +15,21 @@ topological distance to a set of reference pathways.
 
 Arguments:
 >  -h, --help            show this help message and exit
->  --genPathwayGraphlets File where each line is a graphlets file of a
->                        generated pathway. Required.
->  --refPathwayGraphlets File where each line is a graphlets file of a
->                        reference pathway. Required.
+>
+>  --genPathwayGraphlets File where each line is a graphlets file of a generated pathway. Required.
+>
+>  --refPathwayGraphlets File where each line is a graphlets file of a reference pathway. Required.
+>
 >  --outFile OUTFILE     File to store output in. Optional, default = "parameterRanking.txt".
->  --minSize MINSIZE     Minimum size a reference pathway must be to be
->                        rankings. Optional, default=15.
->  --outputMax           If set, will return only the top pathway instead of a
->                        full ranking. Oprional, default = False.
->  --outputScore         If set, will return scores in addition to pathway
->                        rankings. Optional, default = False.
->  --nameMap NAMEMAP     Either a file mapping generated pathway fileNames to
->                        parameter values, "stripped" to exclude the directory
->                        and extension from the filename, or "fileName" to use
->                        raw file names. Optional, default = stripped.
+>
+>  --minSize MINSIZE     Minimum size a reference pathway must be to be rankings. Optional, default=15.
+>
+>  --outputMax           If set, will return only the top pathway instead of a full ranking. Optional, default = False.
+>
+>  --outputScore         If set, will return scores in addition to pathway rankings. Optional, default = False.
+>
+>  --nameMap NAMEMAP     Either a file mapping generated pathway fileNames to parameter values, "stripped" to exclude the directory and extension from the filename, or "fileName" to use raw file names. Optional, default = stripped.
+>
 >  --verbose             If set, will print intermediate status updates. Optional, default = False.
 
 ## Graphlet Creation