Mercurial > repos > cpt > cpt_intersect_adj
changeset 3:10000414e916 draft
planemo upload commit 28919dd79f328dd09dae92661dc19ffa5757a765
| author | cpt |
|---|---|
| date | Mon, 12 Aug 2024 04:23:34 +0000 |
| parents | 0dbc7fbad0ab |
| children | 3e3b5ba626b9 |
| files | intersect_and_adjacent.py intersect_and_adjacent.xml |
| diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/intersect_and_adjacent.py Mon Aug 12 03:04:00 2024 +0000 +++ b/intersect_and_adjacent.py Mon Aug 12 04:23:34 2024 +0000 @@ -268,14 +268,16 @@ 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:
--- a/intersect_and_adjacent.xml Mon Aug 12 03:04:00 2024 +0000 +++ b/intersect_and_adjacent.xml Mon Aug 12 04:23:34 2024 +0000 @@ -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' ]]>