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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f

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+JBrowse2 in Galaxy
+==================
+
+    JBrowse2 is a fast, embeddable genome browser built completely with
+    JavaScript and HTML5
+
+Added April 2024:
+Multiple independent assembly/track sets in the same browser now working
+Tests are now far more convincing using the zip outputs to check for files
+Automated collection generation is really cool - TODO: need visibility for each track
+maf and blastxml are working for test files at least - not yet properly tested.
+cool/mcool are converted to hic 
+vcf, cram, bam, bed, gff, bigwig, hic, cool, blastxml, maf, paf tracks.
+
+
+Added Mar 26:
+Testing history added with tests of the 8 simple formats
+hic and paf need small tests but work with big ones...
+
+Added Mar 8:
+ - URI as data source for tracks
+ - Autogenerate from a collection now builtin to advanced options - ignores form
+    - potentially thousands of tracks without filling in any form...
+ - Cram now working
+ - Multigenome pafs from mashmap working properly..
+ - TODO reuse code for references for paf references to allow URI and builtin genomes
+
+Added Mar 3:
+ - optional tracks at last for JB2
+ - dotted noodles from optional inputs now ignored without harm
+ - autogenJB2.
+    - Takes a collection of bam/vcf etc and turns them into tracks in a normal JB2 history item.
+    - Uses the JbrowseConnector, but the XML tool drives it from the contents of the collection.
+    - Collection can be built from any source or with optional noodles in a WF
+    - Produces a JB2 with all available tracks.
+    - Argparse command line with repeats for tracks and references
+        - so works outside Galaxy to process directories or s3 buckets.
+
+
+Added Feb 3: cool/mcool -> hic
+
+.. image:: dm4_in_jb2.png
+
+Other tracks
+
+.. image:: jb2_samplerMay5.png
+
+JBrowse2 is a fast, embeddable genome browser built completely with
+JavaScript and HTML5
+
+Makes an ideal fit with Galaxy, especially for use as a
+workflow summary. E.g. annotate a genome, then visualise all of the
+associated datasets as an interactive HTML page. This tool MUST be whitelisted
+(or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
+The built-in Galaxy gunicorn server does not support byte range requests, so this tool must be proxied by nginx
+or another web server, correctly configured to support range requests. A tiny web server is bundled
+with each JBrowse2 archive - see below.
+
+Installation
+============
+
+This wrapper is normally installed by a server administrator from the Galaxy Tool Shed IUC JBrowse2 repository.
+
+Local display
+=============
+
+Each JBrowse2 history item can be downloaded ("floppy disk" icon) to your local disk. There, it can be unzipped into a new directory.
+That directory includes a python script, *jb2_webserver.py* that will run a local web server able to serve byte range requests,
+giving the same view as seen when viewed from the Galaxy history.
+
+From the newly unzipped directory where that file can be found, and with Python3 installed and working,
+
+`python3 jb2_webserver.py`
+
+will open the preconfigured browser using the default web browser application.
+
+That webserver code is separately under the Apache 2 license copied in this repository. See below for this code's MIT license.
+
+History
+=======
+
+- 2.10.0+galaxy2
+
+    - UPDATED existing JBrowse1.16.11 code to JBrowse 2.10.0
+    - was working well enough for VGP when previous PR discovered
+        - too late to backport all the fixes
+        - working default session and some other ideas copied instead.
+    - seems to work well with defaults.
+    - need to document and implement track settings by running the browser locally.
+    - works well enough to be useful in workflows such as TreeValGal.
+    - JB2 seems to set defaults wisely.
+    - not yet ideal for users who need fine grained track control.
+    - synteny (paf + reference) now working
+    - rehomed at https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 while IUC reviews are slowly sorted out.
+
+
+Wrapper License (MIT/BSD Style)
+===============================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the names
+of the contributors or copyright holders not be used in advertising or
+publicity pertaining to distribution of the software without specific
+prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR
+CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF
+USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR
+OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR
+PERFORMANCE OF THIS SOFTWARE.