added getCommandInfoCommand for gui

[mothur.git] / pipelinepdscommand.cpp

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index 19e7886bf700eaccf7196a1dd11badfc7365d50a..d1309edde7631d2c8edb0f54c67be9cf02e671d2 100644 (file)
--- 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) {