X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setcurrentcommand.cpp;h=5582abd03d6220da752943278cad50f4bceb1a76;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=16685b24c7c706d0c6cf5aa9d15da2e08e863112;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index 16685b2..5582abd 100644
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -12,7 +12,9 @@
 //**********************************************************************************************************************
 vector<string> SetCurrentCommand::setParameters(){	
 	try {
-			
+		
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+		CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
 		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
 		CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
@@ -81,6 +83,7 @@ SetCurrentCommand::SetCurrentCommand(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 {
 			//valid paramters for this command
@@ -261,6 +264,14 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["taxonomy"] = inputDir + it->second;		}
 				}
+				
+				it = parameters.find("flow");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["flow"] = inputDir + it->second;		}
+				}
 			}
 			
 			//check for parameters
@@ -359,6 +370,15 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
 			else if (taxonomyfile == "not found") {  taxonomyfile = "";  }	
 			if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
 			
+			flowfile = validParameter.validFile(parameters, "flow", true);
+			if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
+			else if (flowfile == "not found") {  flowfile = "";  }	
+			if (flowfile != "") { m->setFlowFile(flowfile); }
+			
+			processors = validParameter.validFile(parameters, "processors", false);
+			if (processors == "not found") {  processors = "1";  }	
+			if (processors != "") { m->setProcessors(processors); }
+			
 			clearTypes = validParameter.validFile(parameters, "clear", false);			
 			if (clearTypes == "not found") { clearTypes = ""; }
 			else { m->splitAtDash(clearTypes, types);	}
@@ -422,6 +442,10 @@ int SetCurrentCommand::execute(){
 					m->setAccnosFile("");
 				}else if (types[i] == "taxonomy") {
 					m->setTaxonomyFile("");
+				}else if (types[i] == "flow") {
+					m->setFlowFile("");
+				}else if (types[i] == "processors") {
+					m->setProcessors("1");
 				}else if (types[i] == "all") {
 					m->clearCurrentFiles();
 				}else {