Mercurial > repos > fubar > jbrowse2

diff jbrowse2.py @ 37:7adde511daa1 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Thu, 29 Feb 2024 00:51:45 +0000
parents 15da358c3108
children 07849bf248e3
line wrap: on
line diff
--- a/jbrowse2.py	Thu Feb 29 00:47:58 2024 +0000
+++ b/jbrowse2.py	Thu Feb 29 00:51:45 2024 +0000
@@ -1137,9 +1137,7 @@
                     outputTrackConfig,
                 )
             elif dataset_ext == "bam":
-                real_indexes = track["conf"]["options"]["bam"]["bam_indices"][
-                    "bam_index"
-                ]
+                real_indexes = track["conf"]["options"]["bam"]["bam_index"]
                 if not isinstance(real_indexes, list):
                     real_indexes = [real_indexes]
 
@@ -1150,7 +1148,7 @@
                     bam_index=real_indexes[i],
                 )
             elif dataset_ext == "cram":
-                real_indexes = track["conf"]["options"]["cram"]["cram_indices"][
+                real_indexes = track["conf"]["options"]["cram"]["cram_index"][
                     "cram_index"
                 ]
                 if not isinstance(real_indexes, list):