diff jbrowse.xml @ 26:08776ba76cf5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5

--- a/jbrowse.xml	Tue Jan 29 05:34:16 2019 -0500
+++ b/jbrowse.xml	Tue Feb 19 15:43:37 2019 -0500
@@ -276,10 +276,6 @@
                     #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>
@@ -461,8 +457,10 @@
 
                 <conditional name="track_config">
                     <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
+                        <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option>
+                        <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option>
                         <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
-                        <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
+                        <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option>
                         <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">
@@ -486,19 +484,12 @@
                                    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>
-                   </when>
-                   <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>
-                  <!--when value="BlastView/View/Track/CanvasFeatures" /-->
+                        </section>
+                    </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" />
                 </conditional>
                 <expand macro="track_styling" />
                 <expand macro="color_selection" />