added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 0955f2dc662dc903c49b34d1fe70103ef8a2b5b0..7ae5d69141979736bcb2b6fcfb25e1ba4682086d 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -16,8 +16,8 @@
 vector<string> ChimeraPerseusCommand::setParameters(){ 
        try {
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
+               CommandParameter pname("name", "InputTypes", "", "", "NameCount", "NameCount", "none",false,false); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none",false,false); parameters.push_back(pcount);
                CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -295,7 +295,7 @@ ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
                                        bool ignore = false;
                                        if (countfileNames[i] == "current") { 
                                                countfileNames[i] = m->getCountTableFile(); 
-                                               if (nameFileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
+                                               if (countfileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
                                                else {  
                                                        m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true; 
                                                        //erase from file list