//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") {
else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listfile == "not open") { listfile = ""; abort = true; }
+ else { m->setListFile(listfile); }
//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"){
namesfile = validParameter.validFile(parameters, "name", true);
if (namesfile == "not open") { abort = true; }
else if (namesfile == "not found") { namesfile = ""; }
+ else { m->setNameFile(namesfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
}
}