helpString += "The default value for label is all lines in your inputfile.\n";
helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
helpString += "The default value for label is all lines in your inputfile.\n";
helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
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->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (fastafile == "not open") { abort = true; }
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") {
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->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; }
//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"){
//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"){
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }