diff jbrowse2.xml @ 112:56f9a6e0fe80 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792

--- a/jbrowse2.xml	Tue Jul 02 05:08:17 2024 +0000
+++ b/jbrowse2.xml	Thu Jul 04 08:40:21 2024 +0000
@@ -8,7 +8,6 @@
         <xref type="bio.tools">jbrowse2</xref>
     </xrefs>
     <expand macro="requirements"/>
-    <expand macro="creators"/>
     <required_files>
         <include path="autogenJB2.py"/>
         <include path="blastxml_to_gapped_gff3.py"/>
@@ -350,8 +349,7 @@
                     <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" 
                         help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
                     </param>
-                    <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4">
-                    </param>
+                    <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
                 </when>
             </conditional>
             <repeat name="track_groups" title="Track Group">
@@ -1152,7 +1150,7 @@
 
 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
 
-At present, 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 
+Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been 
 used to generate the data:
 
     bam
@@ -1198,6 +1196,17 @@
 Annotation Tracks
 -----------------
 
+
+BED
+~~~
+
+Bed feature annotation usually requires clicking on the feature. 
+
+Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5
+set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5 
+for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track.
+
+
 MAF
 ~~~