paralellized the indicator command

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 4bb50ab107bb4fdde1d97b790cd15f3cb42d8599..0704f55896e835f331eda28446012e62c790904e 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -52,7 +52,7 @@ string MetaStatsCommand::getHelpString(){
                helpString += "The metastats command should be in the following format: metastats(design=yourDesignFile).\n";
                helpString += "Example metastats(design=temp.design, groups=A-B-C).\n";
                helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -83,6 +83,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -133,7 +134,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                sharedfile = m->getSharedFile(); 
                                if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        //check for required parameters
                        designfile = validParameter.validFile(parameters, "design", true);
@@ -143,7 +144,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                designfile = m->getDesignFile(); 
                                if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }
+                       }else { m->setDesignFile(designfile); }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){