diff jbrowse.xml @ 27:61ce21e36cb5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46

--- 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" />