diff jbrowse.py @ 16:b5c5470d7c09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5

--- a/jbrowse.py	Wed Jun 14 17:21:28 2017 -0400
+++ b/jbrowse.py	Wed Sep 13 13:07:20 2017 -0400
@@ -436,7 +436,7 @@
 
     def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
         dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
-        cmd = ['ln', data, dest]
+        cmd = ['ln', '-s', data, dest]
         self.subprocess_check_call(cmd)
 
         url = os.path.join('raw', trackData['label'] + '.bw')
@@ -566,7 +566,24 @@
             'category': track['category'],
         }
 
+        mapped_chars = {
+            '>': '__gt__',
+            '<': '__lt__',
+            "'": '__sq__',
+            '"': '__dq__',
+            '[': '__ob__',
+            ']': '__cb__',
+            '{': '__oc__',
+            '}': '__cc__',
+            '@': '__at__',
+            '#': '__pd__'
+        }
+
         for i, (dataset_path, dataset_ext, track_human_label) in enumerate(track['trackfiles']):
+            # 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)
+
             log.info('Processing %s / %s', track['category'], track_human_label)
             outputTrackConfig['key'] = track_human_label
             hashData = [dataset_path, track_human_label, track['category']]