X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pipelinepdscommand.cpp;fp=pipelinepdscommand.cpp;h=d1309edde7631d2c8edb0f54c67be9cf02e671d2;hb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;hp=19e7886bf700eaccf7196a1dd11badfc7365d50a;hpb=c7f5a50aec1ec4b420b286d6ccf980d2a847d494;p=mothur.git

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 19e7886..d1309ed 100644
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -51,7 +51,7 @@ string PipelineCommand::getHelpString(){
 		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"; 
@@ -76,7 +76,7 @@ string PipelineCommand::getHelpString(){
 		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) {