else {
//valid paramters for this command
- string Array[] = {"label","calc","groups","all"};
+ string Array[] = {"label","calc","groups","all","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
mothurOut("You must read a list and a group, or a shared before you can use the summary.shared 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->getSharedFile()); //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...
label = validParameter.validFile(parameters, "label", false);
}
}
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
openOutputFile(outputFileName, outputFileHandle);
mult = false;
}