From b4088a7928f5127bfd34c0cade626d1cd6c9c7ea Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 4 Oct 2017 15:42:17 +0200
Subject: [PATCH] Cython API: Added basic taxonomy option

---
 python/obitools3/apps/optiongroups/__init__.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/python/obitools3/apps/optiongroups/__init__.py b/python/obitools3/apps/optiongroups/__init__.py
index 486e1f6..23fb375 100644
--- a/python/obitools3/apps/optiongroups/__init__.py
+++ b/python/obitools3/apps/optiongroups/__init__.py
@@ -144,7 +144,17 @@ def __addTabularInputOption(optionManager):
                      default=b"#",
                      type=bytes,
                      help="Lines starting by this char are considered as comment")
-  
+
+def __addTaxonomyInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for taxonomy")
+
+    group.add_argument('--taxonomy',
+                     action="store", dest="obi:taxoURI",
+                     default=None,
+                     help="Taxonomy URI")
+    
+    #TODO option bool to download taxo if URI doesn't exist
+    
 def addMinimalInputOption(optionManager):
     __addInputOption(optionManager)
     
@@ -155,11 +165,15 @@ def addSequenceInputOption(optionManager):
 def addTabularInputOption(optionManager):
     __addInputOption(optionManager)
     __addTabularInputOption(optionManager)
-    
+
+def addTaxonomyInputOption(optionManager):
+    __addTaxonomyInputOption(optionManager)
+
 def addAllInputOption(optionManager):
     __addInputOption(optionManager)
     __addSequenceInputOption(optionManager)
     __addTabularInputOption(optionManager)
+    __addTaxonomyInputOption(optionManager)
     
     
 def __addOutputOption(optionManager):