changing command name classify.shared to classifyrf.shared

[mothur.git] / optionparser.cpp

diff --git a/optionparser.cpp b/optionparser.cpp
index e3850e52c56f629a6e5395203f31cc1299a6193b..262ac88286b0639ace8cb3bff4fe10a091ec4748 100644 (file)
--- a/optionparser.cpp
+++ b/optionparser.cpp
@@ -116,6 +116,8 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getDesignFile();
                     }else if (it->first == "sff") {
                         it->second = m->getSFFFile();
+                    }else if (it->first == "flow") {
+                            it->second = m->getFlowFile();
                     }else if (it->first == "oligos") {
                         it->second = m->getOligosFile();
                     }else if (it->first == "accnos") {
@@ -124,8 +126,10 @@ map<string, string> OptionParser::getParameters() {
                         it->second = m->getTaxonomyFile();
                     }else if (it->first == "biom") {
                         it->second = m->getBiomFile();
-                    }else if (it->first == "counttable") {
+                    }else if (it->first == "count") {
                             it->second = m->getCountTableFile();
+                    }else if (it->first == "summary") {
+                            it->second = m->getSummaryFile();
                     }else {
                         m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
                     }