parsimony command now uses groups, fixed bug with unweighted groups

[mothur.git] / helpcommand.cpp

diff --git a/helpcommand.cpp b/helpcommand.cpp
index e5247f90f5dce3a760f39614f77cb4c152ec53f9..b627c140461d19713f39e3907d4d1a14a02b4414 100644 (file)
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -128,8 +128,10 @@ int HelpCommand::execute(){
                cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
        }else if (globaldata->helpRequest == "parsimony") { 
                cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
-               cout << "The parsimony command parameters are random and iters.  No parameters are required." << "\n";
-               cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, iters=yourIters)." << "\n";
+               cout << "The parsimony command parameters are random, groups and iters.  No parameters are required." << "\n";
+               cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group." << "\n";
+               cout << "The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
+               cout << "The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters)." << "\n";
                cout << "Example parsimony(random=out, iters=500)." << "\n";
                cout << "The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony)," << "\n";
                cout << "and iters is 1000.  The parsimony command output three files: .parsimony, .psummary and .pdistrib, their descriptions are in the manual." << "\n";
@@ -137,7 +139,7 @@ int HelpCommand::execute(){
        }else if (globaldata->helpRequest == "unifrac.weighted") { 
                cout << "The unifrac.weighted command can only be executed after a successful read.tree command." << "\n";
                cout << "The unifrac.weighted command parameters are groups and iters.  No parameters are required." << "\n";
-               cout << "The groups paramter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
+               cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups." << "\n";
                cout << "The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
                cout << "The unifrac.weighted command should be in the following format: unifrac.weighted(groups=yourGroups, iters=yourIters)." << "\n";
                cout << "Example unifrac.weighted(groups=A-B-C, iters=500)." << "\n";
@@ -147,7 +149,7 @@ int HelpCommand::execute(){
        }else if (globaldata->helpRequest == "unifrac.unweighted") { 
                cout << "The unifrac.unweighted command can only be executed after a successful read.tree command." << "\n";
                cout << "The unifrac.unweighted command parameters are groups and iters.  No parameters are required." << "\n";
-               cout << "The groups paramter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group." << "\n";
+               cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group." << "\n";
                cout << "The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree." << "\n";
                cout << "The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters)." << "\n";
                cout << "Example unifrac.unweighted(groups=A-B-C, iters=500)." << "\n";