fixed helps

diff --git a/mothur b/mothur
index f9ad770124e3a0b48ff735aac87d252560488e04..ff0d8092bad351f1c68308e2f87fdc18d23ea12e 100755 (executable)
Binary files a/mothur and b/mothur differ

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 1e6643162b5962eadaf1cd36cc0ead26700240ec..59126fb10f24eac3b4c52ac00e5289fedf36fae1 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -120,7 +120,7 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
 
 void ParseFastaQCommand::help(){
        try {
-               m->mothurOut("The fastq.info command reads a fastaQ file and creates a fasta and quality file.\n");
+               m->mothurOut("The fastq.info command reads a fastq file and creates a fasta and quality file.\n");
                m->mothurOut("The fastq.info command parameter is fastq, and it is required.\n");
                m->mothurOut("The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n");
                m->mothurOut("Example fastq.info(fastaq=test.fastaq).\n");

diff --git a/pipelinepdscommand.cpp b/pipelinepdscommand.cpp
index a174cce11a3b4c928c3b08a817d534ad149822bb..b7ba7d382476ade9782660f4b9127c9c1b55b513 100644 (file)
--- a/pipelinepdscommand.cpp
+++ b/pipelinepdscommand.cpp
@@ -183,15 +183,14 @@ void PipelineCommand::help(){
        try {
                 m->mothurOut("The pipeline command is designed to guide you through your analysis using mothur.\n"); 
                 m->mothurOut("The pipeline command parameters are pipeline, sff, oligos, align, chimera, classify, taxonomy and processors.\n"); 
-                m->mothurOut("The sff parameter allows you to enter your sff file. It is required.\n"); 
-                m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required.\n"); 
-                m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required.\n"); 
-                m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required.\n"); 
-                m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required.\n"); 
-                m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required.\n"); 
+                m->mothurOut("The sff parameter allows you to enter your sff file. It is required, if not using pipeline parameter.\n"); 
+                m->mothurOut("The oligos parameter allows you to enter your oligos file. It is required, if not using pipeline parameter.\n"); 
+                m->mothurOut("The align parameter allows you to enter a template to use with the aligner. It is required, if not using pipeline parameter.\n"); 
+                m->mothurOut("The chimera parameter allows you to enter a template to use for chimera detection. It is required, if not using pipeline parameter.\n"); 
+                m->mothurOut("The classify parameter allows you to enter a template to use for classification. It is required, if not using pipeline parameter.\n"); 
+                m->mothurOut("The taxonomy parameter allows you to enter a taxonomy file for the classify template to use for classification. It is required, if not using pipeline parameter.\n"); 
                 m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
                 m->mothurOut("The pipeline parameter allows you to enter your own pipeline file. This file should look like a mothur batchfile, but where you would be using a mothur generated file, you can use mothurmade instead.\n"); 
-                m->mothurOut("First column contains the command name, and the second column contains the parameter options or 'defaults', meaning use defaults. You may leave out file options.\n");
                 m->mothurOut("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");
                 m->mothurOut("then, you could enter unique.seqs(fasta=mothurmade), and mothur would use the .trim.fasta file from the trim.seqs command. \n");
                 m->mothurOut("then you could enter align.seqs(candidate=mothurmade, template=silva.v13.align, processors=8). , and mothur would use the .trim.unique.fasta file from the unique.seqs command. \n");