Mercurial > repos > iuc > jbrowse
changeset 27:61ce21e36cb5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
| author | iuc |
|---|---|
| date | Wed, 20 Feb 2019 11:50:21 -0500 |
| parents | 08776ba76cf5 |
| children | d0743cb18ed8 |
| files | jbrowse.py jbrowse.xml macros.xml |
| diffstat | 3 files changed, 65 insertions(+), 32 deletions(-) [+] |
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--- a/jbrowse.py Tue Feb 19 15:43:37 2019 -0500 +++ b/jbrowse.py Wed Feb 20 11:50:21 2019 -0500 @@ -643,15 +643,19 @@ trackType = 'JBrowse/View/Track/CanvasFeatures' if 'trackType' in gffOpts: trackType = gffOpts['trackType'] - trackData['trackType'] = trackType + trackData['type'] = trackType + trackData['trackType'] = trackType # Probably only used by old jbrowse versions - if trackType == 'JBrowse/View/Track/CanvasFeatures': + if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']: if 'transcriptType' in gffOpts and gffOpts['transcriptType']: trackData['transcriptType'] = gffOpts['transcriptType'] if 'subParts' in gffOpts and gffOpts['subParts']: trackData['subParts'] = gffOpts['subParts'] if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']: trackData['impliedUTRs'] = gffOpts['impliedUTRs'] + elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']: + if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']: + trackData['topLevelFeatures'] = gffOpts['topLevelFeatures'] self._add_track_json(trackData) @@ -820,7 +824,7 @@ if 'GCContent' in data['plugins_python']: self._add_track_json({ - "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta", + "storeClass": "JBrowse/Store/Sequence/IndexedFasta", "type": "GCContent/View/Track/GCContentXY", "label": "GC Content", "key": "GCContentXY", @@ -839,7 +843,7 @@ # TODO: Expose params for everyone. }) self._add_track_json({ - "storeClass": "JBrowse/Store/SeqFeature/IndexedFasta", + "storeClass": "JBrowse/Store/Sequence/IndexedFasta", "type": "GCContent/View/Track/GCContentXY", "label": "GC skew", "key": "GCSkew",
--- a/jbrowse.xml Tue Feb 19 15:43:37 2019 -0500 +++ b/jbrowse.xml Wed Feb 20 11:50:21 2019 -0500 @@ -266,7 +266,7 @@ #else if str($track.data_format.data_format_select) == "gene_calls": <gff> <trackType>${track.data_format.track_config.track_class}</trackType> - #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures': + #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']: #if str($track.data_format.track_config.canvas_options.transcriptType) != "": <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> #end if @@ -276,6 +276,10 @@ #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> #end if + #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']: + #if str($track.data_format.track_config.html_options.topLevelFeatures) != "": + <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures> + #end if #end if #if $track.data_format.match_part.match_part_select: <match>${track.data_format.match_part.name}</match> @@ -464,34 +468,24 @@ <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> </param> <when value="JBrowse/View/Track/CanvasFeatures"> - <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> - <param label="Transcript type" - name="transcriptType" - type="text" - value="" - help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')" - optional="True"/> - <param label="Subfeatures type" - name="subParts" - type="text" - value="" - help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')" - optional="True"/> - <param label="Implied UTRs" - name="impliedUTRs" - type="boolean" - checked="false" - truevalue="true" - falsevalue="false" - 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> + <expand macro="canvas_options" /> + </when> + <when value="JBrowse/View/Track/HTMLFeatures"> + <expand macro="html_options" /> + </when> + <when value="BlastView/View/Track/CanvasFeatures" /> + <when value="NeatHTMLFeatures/View/Track/NeatFeatures"> + <expand macro="html_options" /> </when> - <when value="JBrowse/View/Track/HTMLFeatures" /> - <when value="BlastView/View/Track/CanvasFeatures" /> - <when value="NeatHTMLFeatures/View/Track/NeatFeatures" /> - <when value="NeatCanvasFeatures/View/Track/NeatFeatures" /> + <when value="NeatCanvasFeatures/View/Track/NeatFeatures"> + <expand macro="canvas_options" /> + </when> </conditional> - <expand macro="track_styling" /> + <expand macro="track_styling" + classname="feature2" + label="product,name,id" + description="note,description" + height="10px"/> <expand macro="color_selection" /> <expand macro="track_menu" /> <expand macro="track_display" />
--- a/macros.xml Tue Feb 19 15:43:37 2019 -0500 +++ b/macros.xml Wed Feb 20 11:50:21 2019 -0500 @@ -14,7 +14,7 @@ </requirements> </xml> <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> - <token name="@WRAPPER_VERSION@">galaxy0</token> + <token name="@WRAPPER_VERSION@">galaxy1</token> <token name="@ATTRIBUTION@"><![CDATA[ **Attribution** @@ -385,4 +385,39 @@ <citation type="doi">10.1101/gr.094607.109</citation> </citations> </xml> + + <xml name="canvas_options"> + <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false"> + <param label="Transcript type" + name="transcriptType" + type="text" + value="" + help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')" + optional="True"/> + <param label="Subfeatures type" + name="subParts" + type="text" + value="" + help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')" + optional="True"/> + <param label="Implied UTRs" + name="impliedUTRs" + type="boolean" + checked="false" + truevalue="true" + falsevalue="false" + 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> + </xml> + + <xml name="html_options"> + <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false"> + <param label="Top level features" + name="topLevelFeatures" + type="text" + value="mRNA" + help="Select which top level features should be displayed. If empty, will try to display all features. If your input files represents gene→mRNA→exon/CDS/UTR, you should use mRNA otherwise exons will not be rendered." + optional="True"/> + </section> + </xml> </macros>