From 2f823945594c6e61a7661c253b671a604b8fb959 Mon Sep 17 00:00:00 2001
From: Ross Lazarus <fubar2@users.noreply.github.com>
Date: Tue, 20 Aug 2024 16:29:58 +1000
Subject: [PATCH] update jbrowse2 to 2.13.1  (#1484)
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* adding first tested and working generated tool from https://github.com/fubar2/nftoolmaker
It actually does work. Sort of.
Hope this is useful to someone.

* fixes suggested by bgruening for the PR - all adjustments will now apply to all future generated tools :)

* add yara mapper ToolFactory - NOT from nf-core.
Allows single ended fastq or fasta to be mapped, or a pair of forward and reverse - both must be fastq

* small test files still work :)

* single quotes for $runme - disappeared mysteriously :(

* adding panaroo

* Finally fixed the '$runme' suggestion and got the sanitisers not to.

* fix profile="22.05" - need to update galaxyxml to fix this and the stdio replacement...

* cleanup master branch of fork

* update help
some prompts
add bgperpx - todo add as a parameter

* 2.12.2 update
Add wiggle track colour and other controls
Add bpPerPx in advanced section to control view scale at default open
Clarify dependence on remote URI tabix data if uri source used.

* bump to 2.12.3 jb2
still passes tests - no breakage yet.

* fix JB2VER although not currently used...

* Have the no-build plugin for bed colour above and below zero binary working!
Involved a substantial simplification of the default_session setup - just needed "configuration": displayId in the display.
Simples.

* remove copy for strings.

* Update tools/jbrowse2/jbrowse2.xml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* Update tools/jbrowse2/jbrowse2.xml

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

* fix flake errors and some suggestions

* thought I'd got this one...

* add the new plugin js

* change bed default to not use plugin

* add help explaining relationship to the Bigwig extremes to bed features tool and to the advanced control form.

* update to 2.13.0 release
fix biotools jbrowse entry
informative error message if collection has no fasta reference

* decrement version suffix back to zero

* remove flakery spaces

* make genome from history and built in genome non-optional to fix a sentry issue reported and PR suggested by Marius

* update to 2.13.1 opportunistically :)

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/jbrowse2/jbrowse2.xml | 6 ++++--
 tools/jbrowse2/macros.xml   | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/jbrowse2/jbrowse2.xml b/tools/jbrowse2/jbrowse2.xml
index 93e768b093..e0078c5991 100644
--- a/tools/jbrowse2/jbrowse2.xml
+++ b/tools/jbrowse2/jbrowse2.xml
@@ -335,7 +335,7 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
                         tabix bgzip with predictable index file URI</option>
                 </param>
                 <when value="indexed">
-                    <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
+                    <param name="genome" type="select" optional="false" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome">
                         <options from_data_table="all_fasta">
                             <filter column="2" type="sort_by"/>
                             <validator message="No genomes are available for the selected input dataset" type="no_options"/>
@@ -343,7 +343,7 @@ export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
                     </param>
                 </when>
                 <when value="history">
-                    <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
+                    <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome"/>
                 </when>
                 <when value="uri">
                     <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" 
@@ -1153,6 +1153,8 @@ Browser tracks need a coordinate system, based on the reference genome, so that
 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
     bed
     bigwig
diff --git a/tools/jbrowse2/macros.xml b/tools/jbrowse2/macros.xml
index 7939f4f1e2..cd107511d1 100644
--- a/tools/jbrowse2/macros.xml
+++ b/tools/jbrowse2/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.13.0</token>
+    <token name="@TOOL_VERSION@">2.13.1</token>
     <xml name="edamInc">
         <edam_topics>
             <edam_topic>topic_3307</edam_topic>