cleaned up code

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 19e7886bf700eaccf7196a1dd11badfc7365d50a..968ba4f66a9d233a14e5f579e9563ac4d9bbd706 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -51,7 +51,7 @@ string PipelineCommand::getHelpString(){
                helpString += "Example: trim.seqs(processors=8, allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, fasta=may1.v13.fasta, oligos=may1.v13.oligos, qfile=may1.v13.qual)\n";
                helpString += "then, you could enter unique.seqs(fasta=current), and mothur would use the .trim.fasta file from the trim.seqs command. \n";
                helpString += "then you could enter align.seqs(candidate=current, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n";
-               helpString += "If no pipeline file is given then mothur will use Pat's pipeline. \n\n";
+               helpString += "If no pipeline file is given then mothur will use Pat's pipeline. \n";
                helpString += "Here is a list of the commands used in Pat's pipeline.\n"; 
                helpString += "All paralellized commands will use the processors you entered.\n"; 
                helpString += "The sffinfo command takes your sff file and extracts the fasta and quality files.\n"; 
@@ -76,7 +76,7 @@ string PipelineCommand::getHelpString(){
                helpString += "The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n";
                helpString += "The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n";
                helpString += "The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n";
-               helpString += "\n\n";
+               helpString += "\n";
                return helpString;
        }
        catch(exception& e) {
@@ -94,6 +94,7 @@ PipelineCommand::PipelineCommand(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();
@@ -179,7 +180,7 @@ PipelineCommand::PipelineCommand(string option) {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                        
                        if (pipeFilename != "") {
                                abort = readUsersPipeline();
@@ -187,6 +188,7 @@ PipelineCommand::PipelineCommand(string option) {
                                sffFile = validParameter.validFile(parameters, "sff", true);
                                if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }
                                else if (sffFile == "not open") { sffFile = ""; abort = true; }
+                               else { m->setSFFFile(sffFile); }
                                        
                                oligosFile = validParameter.validFile(parameters, "oligos", true);
                                if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true;  }