changed get.sharedotu to get.sharedseqs

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 14973ccc3c65d05952783acaf3ba03431e842106..51fc0e7b3a93265eee63092adfe5ea75cdb87f6b 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -122,7 +122,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 
                        
                        
-                       if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
+                       if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
                        
 
                }
@@ -168,6 +168,8 @@ void ChimeraSeqsCommand::help(){
                mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n"); 
                mothurOut("\tchimeracheck: \n"); 
                mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n"); 
+               mothurOut("\tchimeraslayer: \n"); 
+               mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); 
                mothurOut("The chimera.seqs command should be in the following format: \n");
                mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
                mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");