X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=helpcommand.cpp;h=05aaff0b0d58a46b380223b5b52ed84812e38c57;hb=2e5ec5cbbd23637ed20da9bdd544d178a3b5d949;hp=8e28cdeb1b1c41c9a9b353f3d8b94439ef3c5c86;hpb=d0939d3ab83988cc068f9ebe60596cf5decb65e5;p=mothur.git

diff --git a/helpcommand.cpp b/helpcommand.cpp
index 8e28cde..05aaff0 100644
--- a/helpcommand.cpp
+++ b/helpcommand.cpp
@@ -72,21 +72,23 @@ int HelpCommand::execute(){
 	}else if (globaldata->helpRequest == "collect.single") {
 		cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
 		cout << "The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
-		cout << "The collect.single command parameters are label, line, freq, calc.  No parameters are required, but you may not use " << "\n";
+		cout << "The collect.single command parameters are label, line, freq, calc and abund.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
 		cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
-		cout << "Example collect(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
+		cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
 		cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << "\n";
 		cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
 		cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "collect.shared") {
 		cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
-		cout << "The collect.shared command parameters are label, line, freq, jumble, calc.  No parameters are required, but you may not use " << "\n";
+		cout << "The collect.shared command parameters are label, line, freq, jumble, calc and groups.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
-		cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators)." << "\n";
-		cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
+		cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+		cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, jumble=1, groups=B-C, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
 		cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile." << "\n";
 		cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "get.group") {
 		cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
@@ -109,26 +111,28 @@ int HelpCommand::execute(){
 	}else if (globaldata->helpRequest == "rarefaction.single") {
 		cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
 		cout << "The rarefaction.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
-		cout << "The rarefaction.single command parameters are label, line, iters, freq, calc.  No parameters are required, but you may not use " << "\n";
+		cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n";
 		cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
-		cout << "Example rarefaction.single(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
+		cout << "Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
 		cout << "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness." << "\n";
 		cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
 		cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "rarefaction.shared") {
 		cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
-		cout << "The rarefaction.shared command parameters are label, line, iters, jumble and calc.  No parameters are required, but you may not use " << "\n";
+		cout << "The rarefaction.shared command parameters are label, line, iters, jumble, groups and calc.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
-		cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators)." << "\n";
-		cout << "Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, jumble=1, calc=sharedobserved)." << "\n";
+		cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+		cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, jumble=1, groups=B-C, calc=sharedobserved)." << "\n";
 		cout << "The default values for iters is 1000, jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n";
+		cout << "The default value for groups is all the groups in your groupfile." << "\n";
 		cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
 	}else if (globaldata->helpRequest == "summary.single") { 
 		cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
 		cout << "The summary.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster." << "\n";
-		cout << "The summary.single command parameters are label, line, calc.  No parameters are required, but you may not use " << "\n";
+		cout << "The summary.single command parameters are label, line, calc, abund.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
 		cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
 		cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
@@ -139,10 +143,12 @@ int HelpCommand::execute(){
 		cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
 		cout << "The summary.shared command parameters are label, line, jumble and calc.  No parameters are required, but you may not use " << "\n";
 		cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
-		cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators)." << "\n";
-		cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
+		cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+		cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, groups=B-C, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
 		cout << "The default value for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble) and calc is sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN" << "\n";
+		cout << "The default value for groups is all the groups in your groupfile." << "\n";
 		cout << "The label and line parameters are used to analyze specific lines in your input." << "\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 << "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";