Mercurial > repos > fubar > jbrowse2

diff jbrowse2.py @ 30:8f02a84ee278 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
author fubar
date Wed, 21 Feb 2024 02:57:30 +0000
parents f728cf0df71d
children cb4b32ca9968
line wrap: on
line diff
--- a/jbrowse2.py	Fri Feb 16 00:04:37 2024 +0000
+++ b/jbrowse2.py	Wed Feb 21 02:57:30 2024 +0000
@@ -1119,6 +1119,7 @@
             # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
             for key, value in mapped_chars.items():
                 track_human_label = track_human_label.replace(value, key)
+            track_human_label = track_human_label.replace(" ","_")
             outputTrackConfig = {
                 "category": category,
                 "style": {},
@@ -1141,13 +1142,13 @@
                     dataset_ext,
                     outputTrackConfig,
                 )
-            elif dataset_ext in ("hic",):
+            elif dataset_ext in ("hic","juicebox_hic"):
                 self.add_hic(
                     dataset_path,
                     outputTrackConfig,
                 )
             elif dataset_ext in ("cool", "mcool", "scool"):
-                hic_url = "%s_%d.hic" % (track_human_label, i)
+                hic_url = "%s_%d.juicebox_hic" % (track_human_label, i)
                 hic_path = os.path.join(self.outdir, hic_url)
                 self.subprocess_check_call(
                     [