X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=02d8413675bade0cf79f8781987cc45078b74db2;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=2312649d1cff739956638ba2ad8788949669f1d5;hpb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;p=mothur.git

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 2312649..02d8413 100644
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -46,8 +46,8 @@ string GetSharedOTUCommand::getHelpString(){
 		helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
 		helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
 		helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
-		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
-		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
 		helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
 		helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
 		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";