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);
globaldata->Groups = Groups;
}
- string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "true"; }
+ string temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
all = isTrue(temp);
if (abort == false) {
}
}
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "shared.summary";
openOutputFile(outputFileName, outputFileHandle);
mult = false;
}
mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
mothurOut("The default value for groups is all the groups in your groupfile.\n");
mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is true.\n");
+ mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
mothurOut("If you use sharedchao and run into memory issues, set all to false. \n");
mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");