+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("qfile");
+ //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["qfile"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ fastaFileName = validParameter.validFile(parameters, "fasta", true);
+ if (fastaFileName == "not open") { abort = true; }
+ else if (fastaFileName == "not found") { fastaFileName = "";}// m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
+
+ qualFileName = validParameter.validFile(parameters, "qfile", true);
+ if (qualFileName == "not open") { abort = true; }
+ else if (qualFileName == "not found") { qualFileName = ""; }//m->mothurOut("fasta is a required parameter for the reverse.seqs command."); m->mothurOutEndLine(); abort = true; }
+
+ if((fastaFileName == "") && (qualFileName == "")){
+ fastaFileName = m->getFastaFile();
+ if (fastaFileName != "") { m->mothurOut("Using " + fastaFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else {
+ qualFileName = m->getQualFile();
+ if (qualFileName != "") { m->mothurOut("Using " + qualFileName + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current files for fasta or qfile, and fasta or qfile is a required parameter for the reverse.seqs command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReverseSeqsCommand", "ReverseSeqsCommand");
+ exit(1);
+ }
+}