Mercurial > repos > iuc > paffy_tile
diff paffy_tile.xml @ 1:03da093291cf draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/paffy commit 9eb0e8172b3ac29d96aa9f28a89bc1d60fc11ec6
| author | iuc |
|---|---|
| date | Thu, 05 Mar 2026 14:19:03 +0000 |
| parents | 0f451c5e1128 |
| children |
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--- a/paffy_tile.xml Wed Mar 04 13:14:58 2026 +0000 +++ b/paffy_tile.xml Thu Mar 05 14:19:03 2026 +0000 @@ -60,7 +60,7 @@ Overlapping or lower-quality alignments for the same sequence receive higher levels (e.g., 2, 3). To determine priority, alignments are first sorted by their chain score (tag: 's1') if available, or otherwise by their alignment score (tag: 'AS'). -As output PAF file, a new PAF file is generated where alignments are sorted by their score and additonally annotated with two tags: +As output, a new PAF file is generated where alignments are sorted by their score and additonally annotated with two tags: * **tp (Type of alignment):** Indicates if the alignment is (P)rimary, (S)econdary, or an (I)nversion. Note that the 'I' state is not generated by Paffy itself but is preserved if set by a previous tool. * **tl (Tile level):** Indicates the alignment's rank for covering the sequence. A level of 1 represents the best (optimal) alignment, level 2 is the second best, etc.