diff jbrowse.xml @ 13:69c5e9c0add0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79

--- 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" />