X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;h=84282dcc39105c7f4d560b88fcacdcb4ed4342d6;hb=7c08fa69c0b89e7a08341af2aa724f206f182075;hp=ae2663df8e63b117995b3442227f72343e194bbb;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index ae2663d..84282dc 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -49,10 +49,10 @@ vector<string> PipelineCommand::getRequiredFiles(){
 PipelineCommand::PipelineCommand(string option) {
 	try {
 		cFactory = CommandFactory::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			
@@ -183,15 +183,14 @@ void PipelineCommand::help(){
 	try {
 		 m->mothurOut("The pipeline command is designed to guide you through your analysis using mothur.\n"); 
 		 m->mothurOut("The pipeline command parameters are pipeline, sff, oligos, align, chimera, classify, taxonomy and processors.\n"); 
-		 m->mothurOut("The sff parameter allows you to enter your sff file. It is required.\n"); 
-		 m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required.\n"); 
-		 m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required.\n"); 
-		 m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required.\n"); 
-		 m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required.\n"); 
-		 m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required.\n"); 
+		 m->mothurOut("The sff parameter allows you to enter your sff file. It is required, if not using pipeline parameter.\n"); 
+		 m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required, if not using pipeline parameter.\n"); 
+		 m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required, if not using pipeline parameter.\n"); 
+		 m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required, if not using pipeline parameter.\n"); 
+		 m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required, if not using pipeline parameter.\n"); 
+		 m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required, if not using pipeline parameter.\n"); 
 		 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
 		 m->mothurOut("The pipeline parameter allows you to enter your own pipeline file. This file should look like a mothur batchfile, but where you would be using a mothur generated file, you can use mothurmade instead.\n"); 
-		 m->mothurOut("First column contains the command name, and the second column contains the parameter options or 'defaults', meaning use defaults. You may leave out file options.\n");
 		 m->mothurOut("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");
 		 m->mothurOut("then, you could enter unique.seqs(fasta=mothurmade), and mothur would use the .trim.fasta file from the trim.seqs command. \n");
 		 m->mothurOut("then you could enter align.seqs(candidate=mothurmade, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n");
@@ -236,7 +235,7 @@ PipelineCommand::~PipelineCommand(){}
 
 int PipelineCommand::execute(){
 	try {
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int start = time(NULL);
 		
@@ -358,6 +357,8 @@ bool PipelineCommand::checkForValidAndRequiredParameters(string name, string opt
 				
 		if (name == "system") { return false; }
 		
+		if (name == "system") { return false; }
+		
 		//get shell of the command so we can check to make sure its valid without running it
 		Command* command = cFactory->getCommand(name);
 			
@@ -524,6 +525,8 @@ int PipelineCommand::runUsersPipeline(){
 		}
 		
 		in.close();
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PipelineCommand", "runUsersPipeline");