X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makefastqcommand.cpp;fp=makefastqcommand.cpp;h=18ca8644a2f0bfffc1035706c7a6b46df8aba043;hb=002421a439168e2610a2b62f1318f21c7202fe6d;hp=3809af2a55e6e959014f271ce1ee642854a336aa;hpb=5890a0d1e8f3a549652abc18a2f34d65b3ce7075;p=mothur.git

diff --git a/makefastqcommand.cpp b/makefastqcommand.cpp
index 3809af2..18ca864 100644
--- a/makefastqcommand.cpp
+++ b/makefastqcommand.cpp
@@ -142,15 +142,12 @@ MakeFastQCommand::MakeFastQCommand(string option)  {
 
 void MakeFastQCommand::help(){
 	try {
-		/*m->mothurOut("The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
-		m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
-		m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
+		m->mothurOut("The make.fastq command read a fasta and quality file and creates a fastq file.\n");
+		m->mothurOut("The make.fastq command parameters are fasta and qfile, both are required.\n");
 		m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
-		m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like.  You can separate group names with dashes.\n");
-		m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
-		m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
-		m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
-		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");*/
+		m->mothurOut("The make.fastq command should be in the following format: make.fastq(qfile=yourQualityFile, fasta=yourFasta).\n");
+		m->mothurOut("Example make.fastq(fasta=amazon.fasta, qfile=amazon.qual).\n");
+		m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 	}
 	catch(exception& e) {
 		m->errorOut(e, "MakeFastQCommand", "help");