-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, 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("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");
- m->mothurOut("If no pipeline file is given then mothur will use Pat's pipeline. \n\n");
- m->mothurOut("Here is a list of the commands used in Pat's pipeline.\n");
- m->mothurOut("All paralellized commands will use the processors you entered.\n");
- m->mothurOut("The sffinfo command takes your sff file and extracts the fasta and quality files.\n");
- m->mothurOut("The trim.seqs command uses your oligos file and the quality and fasta files generated by sffinfo.\n");
- m->mothurOut("The trim.seqs command sets the following parameters: allfiles=T, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50.\n");
- m->mothurOut("The unique.seqs command uses the trimmed fasta file and removes redundant sequences, don't worry the names file generated by unique.seqs will be used in the pipeline to make sure they are included.\n");
- m->mothurOut("The align.seqs command aligns the unique sequences using the aligners default options. \n");
- m->mothurOut("The screen.seqs command screens the sequences using optimize=end-minlength. \n");
- m->mothurOut("The pipeline uses chimera.slayer to detect chimeras using the default options. \n");
- m->mothurOut("The pipeline removes all sequences determined to be chimeric by chimera.slayer. \n");
- m->mothurOut("The filter.seqs command filters the sequences using vertical=T, trump=. \n");
- m->mothurOut("The unique.seqs command uses the filtered fasta file and name file to remove sequences that have become redundant after filtering.\n");
- m->mothurOut("The pre.cluster command clusters sequences that have no more than 2 differences.\n");
- m->mothurOut("The dist.seqs command is used to generate a column and phylip formatted distance matrix using cutoff=0.20 for column.\n");
- m->mothurOut("The pipeline uses cluster with method=average, hard=T. \n");
- m->mothurOut("The classify.seqs command is used to classify the sequences using the bayesian method with a cutoff of 80.\n");
- m->mothurOut("The phylotype command is used to cluster the sequences based on their classification.\n");
- m->mothurOut("The clearcut command is used to generate a tree using neighbor=T. \n");
- m->mothurOut("The summary.single and summary.shared commands are run on the otu files from cluster and phylotype commands. \n");
- m->mothurOut("The summary.shared command uses calc=sharednseqs-sharedsobs-sharedchao-sharedace-anderberg-jclass-jest-kulczynski-kulczynskicody-lennon-ochiai-sorclass-sorest-whittaker-braycurtis-jabund-morisitahorn-sorabund-thetan-thetayc. \n");
- m->mothurOut("The summary.single command uses calc=nseqs-sobs-coverage-bergerparker-chao-ace-jack-bootstrap-boneh-efron-shen-solow-shannon-npshannon-invsimpson-qstat-simpsoneven-shannoneven-heip-smithwilson. \n");
- m->mothurOut("The classify.otu command is used to get the concensus taxonomy for otu files from cluster and phylotype commands. \n");
- m->mothurOut("The phylo.diversity command run on the tree generated by clearcut with rarefy=T, iters=100. \n");
- m->mothurOut("The unifrac commands are also run on the tree generated by clearcut with random=F, distance=T. \n");
- m->mothurOut("\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "PipelineCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-PipelineCommand::~PipelineCommand(){}
-
-//**********************************************************************************************************************
-