try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pfasta);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","fastq",false,true,true); parameters.push_back(pqfile);
- CommandParameter pformat("format", "Multiple", "sanger-illumina", "sanger", "", "", "","",false,false); parameters.push_back(pformat);
+ CommandParameter pformat("format", "Multiple", "sanger-illumina-illumina1.8+", "sanger", "", "", "","",false,false); parameters.push_back(pformat);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string helpString = "";
helpString += "The make.fastq command reads a fasta and quality file and creates a fastq file.\n";
helpString += "The make.fastq command parameters are fasta, qfile and format. fasta and qfile are required.\n";
- helpString += "The format parameter is used to indicate whether your sequences are sanger or illumina, default=sanger.\n";
+ helpString += "The format parameter is used to indicate whether your sequences are sanger, illumina1.8+ or illumina, default=sanger.\n";
helpString += "The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n";
helpString += "Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
format = validParameter.validFile(parameters, "format", false); if (format == "not found"){ format = "sanger"; }
- if ((format != "sanger") && (format != "illumina") && (format != "solexa")) {
- m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+ if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+")) {
+ m->mothurOut(format + " is not a valid format. Your format choices are sanger, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
abort=true;
}