--- a/jbrowse2.xml	Wed Jun 05 10:00:07 2024 +0000
+++ b/jbrowse2.xml	Fri Jun 21 23:34:31 2024 +0000
@@ -8,6 +8,7 @@
         <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"/>
@@ -28,9 +29,9 @@
         #if $autoCollection[$key].is_collection:
             #set subCol=$autoCollection[$key]
             #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
+            #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in ['fasta.gz','fasta']]
             #if len($pafs) > 0:
                 --pafmeta '$pafs[0]'
-                #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
                 #for $ref in $refs:
                     --pafreferencemeta '$ref'
                 #end for
@@ -314,7 +315,7 @@
 ]]></configfile>
     </configfiles>
     <inputs>
-        <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files">
+        <repeat name="assemblies" min="1" title="Genome for a set of tracks" help="Tracks will display on this genome coordinates so must all match. Multiple genomes with their own sets of tracks can be added">
             <conditional name="reference_genome">
                 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track">
                     <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
@@ -334,8 +335,11 @@
                     <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
                 </when>
                 <when value="uri">
-                    <param name="uri" type="text" label="URI pointing to tabix compressed fasta"/>
-                    <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
+                    <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>
                 </when>
             </conditional>
             <repeat name="track_groups" title="Track Group">
@@ -343,16 +347,16 @@
                 <repeat name="data_tracks" title="Annotation Track">
                     <conditional name="data_format" label="Track Data Selection Options">
                         <param name="data_format_select" type="select" label="Track Type">
-                            <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
+                            <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
                             <option value="bed">BED track</option>
                             <option value="bigwig">BigWig track</option>
                             <option value="blastxml">Blast XML track (as GFF3)</option>
-                            <option value="cram">CRAM track, we recomment to convert to BED like for BAM</option>
+                            <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
                             <option value="gff">GFF/GFF3 track</option>
                             <option value="cool">HiC as cool/mcool/scool format files</option>
                             <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
                             <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
-                            <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
+                            <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option>
                             <option value="vcf">VCF SNP track</option>
                         </param>
                         <when value="blastxml">
@@ -404,6 +408,7 @@
                         <when value="bigwig">
                             <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
                             <expand macro="track_visibility"/>
+                            <expand macro="track_styling_bigwig"/>                            
                         </when>
                         <when value="paf">
                             <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
@@ -1129,29 +1134,31 @@
 
 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
 
-Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
-and detailed track styling is not yet implemented. Please contact us if you are missing features.
 
 Use and local viewing
 =====================
 
+All tracks have a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
+There are 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 
+used to generate the data:
+
+    bam
+    bed
+    bigwig
+    blastxml
+    cram
+    gff3
+    hic
+    maf
+    paf
+    vcf
+
+cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. 
+Otherwise conversion to bed is recommended to slim them down. 
+Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. 
 
 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
 
-The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
-This can be shared and viewed without Galaxy.
-
-A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
-assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
-directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
-
-With python3 installed,
-
-*python3 jb2_webserver.py*
-
-will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
-but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
-
 Overview
 --------
 
@@ -1175,6 +1182,7 @@
 
 **Track Groups** represent a set of tracks in a single category.
 
+
 Annotation Tracks
 -----------------
 
@@ -1232,6 +1240,22 @@
 **Protein blast search** option merely informs underlying tools that
 they should adjust feature locations by 3x.
 
+Local viewing
+=============
+
+The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
+This can be shared and viewed without Galaxy.
+
+A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
+assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
+directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
+
+With python3 installed,
+
+*python3 jb2_webserver.py*
+
+will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
+but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
 
 ]]></help>
     <expand macro="citations"/>