X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=968ba4f66a9d233a14e5f579e9563ac4d9bbd706;hb=cc19310422f125d6628980bd1148e1e816792382;hp=19e7886bf700eaccf7196a1dd11badfc7365d50a;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 19e7886..968ba4f 100644
--- 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;  }