adding code for ambiguous nucleotides

richard-burhans · Apr 16, 2024 · f51af96 · f51af96
1 parent d6b9d4e
commit f51af96
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/tools/segalign/segalign.xml b/tools/segalign/segalign.xml
@@ -58,6 +58,14 @@ OMP_THREAD_LIMIT=\${GALAXY_SLOTS:-2}
 #if $scoring_pathname != "None":
             --scoring '$scoring_pathname'
 #end if
+#if str($mode.scoring_options.ambiguous_selector) != "x"
+    #if str($mode.scoring_options.set_ambiguous_params_selector) == "true"
+        #set $argument_value = ','.join($mode.scoring_options.ambiguous_selector, $mode.scoring_options.ambiguous_reward, $mode.scoring_options.ambiguous_penalty)
+            --ambiguous '$argument_value'
+    #else
+            --ambiguous '$ambiguous_selector'
+    #end if
+#end if
 
 ## Seeding Options -----------------------------------------------------