if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 = ""; }
-
-
//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 = ""; }
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); 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 = ""; }
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; }
else { m->splitAtDash(groups, groupsNames); }
try {
if (abort == true) { return 0; }
+ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
+
+ filename = outputDir + filename;
+
ofstream out;
m->openOutputFile(filename, out);