helpString += "Example: trim.seqs(processors=8, allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, fasta=may1.v13.fasta, oligos=may1.v13.oligos, qfile=may1.v13.qual)\n";
helpString += "then, you could enter unique.seqs(fasta=current), and mothur would use the .trim.fasta file from the trim.seqs command. \n";
helpString += "then you could enter align.seqs(candidate=current, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n";
- helpString += "If no pipeline file is given then mothur will use Pat's pipeline. \n\n";
+ helpString += "If no pipeline file is given then mothur will use Pat's pipeline. \n";
helpString += "Here is a list of the commands used in Pat's pipeline.\n";
helpString += "All paralellized commands will use the processors you entered.\n";
helpString += "The sffinfo command takes your sff file and extracts the fasta and quality files.\n";
helpString += "The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n";
helpString += "The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n";
helpString += "The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n";
- helpString += "\n\n";
+ helpString += "\n";
return helpString;
}
catch(exception& e) {
//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();
sffFile = validParameter.validFile(parameters, "sff", true);
if (sffFile == "not found") { m->mothurOut("sff is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }
else if (sffFile == "not open") { sffFile = ""; abort = true; }
+ else { m->setSFFFile(sffFile); }
oligosFile = validParameter.validFile(parameters, "oligos", true);
if (oligosFile == "not found") { m->mothurOut("oligos is a required parameter for the pipeline command."); m->mothurOutEndLine(); abort = true; }