# HG changeset patch # User iuc # Date 1486661776 18000 # Node ID 69c5e9c0add0e84c00dbc2bf46307b4fc6d769e2 # Parent db5fe5a3176a9129723bf0da78fe3180f9c11cc9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 diff -r db5fe5a3176a -r 69c5e9c0add0 jbrowse.py --- a/jbrowse.py Mon Feb 06 12:52:09 2017 -0500 +++ b/jbrowse.py Thu Feb 09 12:36:16 2017 -0500 @@ -424,6 +424,10 @@ '--trackType', 'JBrowse/View/Track/CanvasFeatures' ] + # className in --clientConfig is ignored, it needs to be set with --className + if 'className' in trackData['style']: + cmd += ['--className', trackData['style']['className']] + self.subprocess_check_call(cmd) os.unlink(gff3) @@ -506,6 +510,10 @@ '--key', trackData['key'] ] + # className in --clientConfig is ignored, it needs to be set with --className + if 'className' in trackData['style']: + cmd += ['--className', trackData['style']['className']] + config = copy.copy(trackData) clientConfig = trackData['style'] del config['style'] @@ -528,6 +536,9 @@ config['subParts'] = gffOpts['subParts'] if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: config['impliedUTRs'] = gffOpts['impliedUTRs'] + elif trackType == 'JBrowse/View/Track/HTMLFeatures': + if 'transcriptType' in gffOpts and gffOpts['transcriptType']: + cmd += ['--type', gffOpts['transcriptType']] cmd += [ '--trackType', gffOpts['trackType'] diff -r db5fe5a3176a -r 69c5e9c0add0 jbrowse.xml --- a/jbrowse.xml Mon Feb 06 12:52:09 2017 -0500 +++ b/jbrowse.xml Thu Feb 09 12:36:16 2017 -0500 @@ -227,6 +227,10 @@ #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": ${track.data_format.track_config.canvas_options.impliedUTRs} #end if + #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures': + #if str($track.data_format.track_config.html_options.transcriptType) != "": + ${track.data_format.track_config.html_options.transcriptType} + #end if #end if #if $track.data_format.match_part.match_part_select: ${track.data_format.match_part.name} @@ -420,7 +424,16 @@ help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/> - + +
+ +
+