testing 1.14.0

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 22f5a97b498187b23b651695e8b3d9a1b8cef1f6..691d35d84f2040c4c10dabe37990d70e90c26e1a 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -536,18 +536,23 @@ bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<strin
                
                //fill in mothurmade filenames
                for (it = parameters.begin(); it != parameters.end(); it++) { 
+                       string paraType = it->first;
+                       
                        if (it->second == "mothurmade") {
-                               itMade = mothurMadeFiles.find(it->first);
+                               
+                               if (it->first == "candidate") { paraType = "fasta"; }
+                       
+                               itMade = mothurMadeFiles.find(paraType);
                                
                                if (itMade == mothurMadeFiles.end()) { 
-                                       m->mothurOut("Looking for a mothurmade " + it->first + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine();
+                                       m->mothurOut("Looking for a mothurmade " + paraType + " file, but it seems mothur has not made that file type in your current pipeline, please correct."); m->mothurOutEndLine();
                                        return true;
                                }else{
                                        vector<string> temp = itMade->second;
                                        
                                        if (temp.size() > 1) {
                                                //ask user which file to use
-                                               m->mothurOut("More than one file has been created for the " + it->first + " parameter. "); m->mothurOutEndLine();
+                                               m->mothurOut("More than one file has been created for the " + paraType + " parameter. "); m->mothurOutEndLine();
                                                for (int i = 0; i < temp.size(); i++) {
                                                        m->mothurOut(toString(i) + " - " + temp[i]); m->mothurOutEndLine();
                                                }
@@ -558,7 +563,7 @@ bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<strin
                                                
                                                if ((num < 0) || (num > (temp.size()-1))) { m->mothurOut("Not a valid response, quitting."); m->mothurOutEndLine(); return true; }
                                                else {
-                                                       parameters[it->first] = temp[num];
+                                                       parameters[paraType] = temp[num];
                                                }
                                
                                                //clears buffer so next command doesn't have error
@@ -566,15 +571,15 @@ bool PipelineCommand::fillInMothurMade(string& options, map<string, vector<strin
                                                getline(cin, s);
                                                
                                        }else if (temp.size() == 0){
-                                               m->mothurOut("Sorry, we seem to think you created a " + it->first + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine();
+                                               m->mothurOut("Sorry, we seem to think you created a " + paraType + " file, but it seems mothur doesn't have a filename."); m->mothurOutEndLine();
                                                return true;
                                        }else{
-                                               parameters[it->first] = temp[0];
+                                               parameters[paraType] = temp[0];
                                        }
                                }
                        }
                        
-                       options += it->first + "=" + parameters[it->first] + ", ";
+                       options += it->first + "=" + parameters[paraType] + ", ";
                }
                
                //rip off extra comma
@@ -594,13 +599,13 @@ void PipelineCommand::createPatsPipeline(){
                
                //sff.info command
                string thisCommand = "sffinfo(sff=" + sffFile + ")";
-               //commands.push_back(thisCommand);
+               commands.push_back(thisCommand);
                
                //trim.seqs command
                string fastaFile = m->getRootName(m->getSimpleName(sffFile)) + "fasta";
                string qualFile = m->getRootName(m->getSimpleName(sffFile)) + "qual";
-               //thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
-               //commands.push_back(thisCommand);
+               thisCommand = "trim.seqs(processors=" + toString(processors) + ", fasta=" + fastaFile + ", allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, oligos=" + oligosFile + ", qfile=" + qualFile + ")";
+               commands.push_back(thisCommand);
                
                //unique.seqs
                string groupFile = m->getRootName(m->getSimpleName(fastaFile)) + "groups";