| Previous changeset 12:db5fe5a3176a (2017-02-06) Next changeset 14:18be2d72fdee (2017-06-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 |
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modified:
jbrowse.py jbrowse.xml |
| b |
| 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 |
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| @@ -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'] |
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| 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($track.data_format.track_config.canvas_options.impliedUTRs) != "false": <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</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) != "": + <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType> + #end if #end if #if $track.data_format.match_part.match_part_select: <match>${track.data_format.match_part.name}</match> @@ -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"/> </section> </when> - <when value="JBrowse/View/Track/HTMLFeatures" /> + <when value="JBrowse/View/Track/HTMLFeatures"> + <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false"> + <param label="Transcript type" + name="transcriptType" + type="text" + value="" + help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')" + optional="True"/> + </section> + </when> </conditional> <expand macro="track_styling" /> <expand macro="color_selection" /> |