X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pipelinepdscommand.cpp;h=958201d0f5590118e26897613f3d0b0ed384abe9;hp=898ad9b72640a4f5c9050f98b399e23efeafd58d;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 898ad9b..958201d 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -14,16 +14,16 @@
 //**********************************************************************************************************************
 vector<string> PipelineCommand::setParameters(){	
 	try {
-		CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(psff);
-		CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(poligos);
-		CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(palign);
-		CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pchimera);
-		CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(pclassify);
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe",false,false); parameters.push_back(ptaxonomy);
-		CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none",false,false); parameters.push_back(ppipeline);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter psff("sff", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(psff);
+		CommandParameter poligos("oligos", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(poligos);
+		CommandParameter palign("align", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(palign);
+		CommandParameter pchimera("chimera", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pchimera);
+		CommandParameter pclassify("classify", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(pclassify);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "oneRequired", "pipe","",false,false,true); parameters.push_back(ptaxonomy);
+		CommandParameter ppipeline("pipeline", "InputTypes", "", "", "none", "oneRequired", "none","",false,false,true); parameters.push_back(ppipeline);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -180,7 +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();