From: westcott Date: Wed, 27 Oct 2010 16:03:59 +0000 (+0000) Subject: fixed helps X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=432ddfdccc4ca0ed83c62747956a472af29e9183 fixed helps --- diff --git a/mothur b/mothur index f9ad770..ff0d809 100755 Binary files a/mothur and b/mothur differ diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp index 1e66431..59126fb 100644 --- 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 a174cce..b7ba7d3 100644 --- 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");