diff --git a/Readme.md b/Readme.md index bd62b95..cf09fc9 100644 --- a/Readme.md +++ b/Readme.md @@ -26,7 +26,10 @@ MzidToTsvConverter uses PSI_Interface.dll to read the mzid file. ### Optional parameters: `-tsv:path` -* Path to the tsv file to be written. If not specified, will be created in the same location as the .mzid file. +* Path to tsv file to be written + * Can be a filename, a directory path, or a file path +* If not specified, will be output to the same location as the mzid. +* If mzid path is a directory, this will be treated as a directory path `-unroll` or `-u` * Signifies that results should be unrolled, giving one line per unique peptide/protein combination in each spectrum identification @@ -49,7 +52,8 @@ MzidToTsvConverter uses PSI_Interface.dll to read the mzid file. * For example, -qvalue:0.001 `-noExtended` or `-ne` -* Do not output the extended fields (e.g., Scan Time). When this flag is specified the output will have the same columns as the MS-GF+ MzidToTsv output, and be a near match when run with the same parameters +* Do not output the extended fields (e.g., Scan Time) +* When this flag is specified, the output will have the same columns as the MS-GF+ MzidToTsv output, and be a near match when run with the same parameters `-recurse` or `-r` * If mzid path is a directory, specifying this will cause mzid files in subdirectories to also be converted.