else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","calc", "abund"};
+ string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); 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 = "";
+ outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
}
}
- venn = new Venn();
+ venn = new Venn(outputDir);
}
}