Mercurial > repos > iuc > jbrowse
changeset 16:b5c5470d7c09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
| author | iuc |
|---|---|
| date | Wed, 13 Sep 2017 13:07:20 -0400 |
| parents | 4e11a688a635 |
| children | ff11d442feed |
| files | jbrowse.py jbrowse.xml |
| diffstat | 2 files changed, 19 insertions(+), 2 deletions(-) [+] |
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--- 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']]
--- a/jbrowse.xml Wed Jun 14 17:21:28 2017 -0400 +++ b/jbrowse.xml Wed Sep 13 13:07:20 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.1"> +<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.2"> <description>genome browser</description> <macros> <import>macros.xml</import>