# HG changeset patch
# User iuc
# Date 1550681421 18000
# Node ID 61ce21e36cb54dcab39d63051deab00a5c22c951
# Parent  08776ba76cf551704f9f4df1c15b4df60114a569
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46

diff -r 08776ba76cf5 -r 61ce21e36cb5 jbrowse.py
--- 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",
diff -r 08776ba76cf5 -r 61ce21e36cb5 jbrowse.xml
--- 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" />
diff -r 08776ba76cf5 -r 61ce21e36cb5 macros.xml
--- 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>