Fixes stranding arg

Command line execution was getting empty string, causing failures [#15]
TAMU-CPT · Aug 12, 2024 · 28919dd · 28919dd
1 parent 48284d6
commit 28919dd
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/cpt_intersect_adj/intersect_and_adjacent.py b/cpt_intersect_adj/intersect_and_adjacent.py
@@ -268,14 +268,16 @@ def intersect(a, b, window, stranding):
         help="Allows features this far away to still be considered 'adjacent'",
     )
     parser.add_argument(
-        "-stranding",
-        action="store_true",
-        help="Only allow adjacency for same-strand features",
+        "stranding",
+        nargs="?",
+        default="",
+        help="Only allow adjacency for same-strand features if set to '-stranding'",
     )
     parser.add_argument("--oa", type=str, default="a_hits_near_b.gff")
     parser.add_argument("--ob", type=str, default="b_hits_near_a.gff")
     args = parser.parse_args()
 
+    stranding = args.stranding == "-stranding"
     b, a = intersect(args.a, args.b, args.window, args.stranding)
 
     with open(args.oa, "w") as handle:

diff --git a/cpt_intersect_adj/intersect_and_adjacent.xml b/cpt_intersect_adj/intersect_and_adjacent.xml
@@ -10,8 +10,8 @@
     python '$__tool_directory__/intersect_and_adjacent.py'
     '$gff3_data_a'
     '$gff3_data_b'
-    '$window'
-    '$stranding'
+    $window
+    $stranding
     --oa '$oa'
     --ob '$ob'
     ]]>