X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=optionparser.cpp;h=e3850e52c56f629a6e5395203f31cc1299a6193b;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=2d13cd0cc5d2e1706d424c92440cd97c426b8fa8;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/optionparser.cpp b/optionparser.cpp
index 2d13cd0..e3850e5 100644
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -124,6 +124,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getTaxonomyFile();
                     }else if (it->first == "biom") {
                         it->second = m->getBiomFile();
+                    }else if (it->first == "counttable") {
+                            it->second = m->getCountTableFile();
                     }else {
                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
                     }