--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/autogenJB2.xml	Tue Jan 30 06:05:03 2024 +0000
@@ -0,0 +1,148 @@
+ <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05">
+    <description>Files to JBrowse2</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edamInc"/>
+    <xrefs>
+        <xref type="bio.tools">jbrowse2</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+python '$__tool_directory__/autogenJB2.py'
+--outdir '$jbrowseme'
+
+&&
+
+cp '$output.files_path/index.html' '$output'
+
+## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
+#if str($uglyTestingHack) == "enabled":
+ &&   cp '$trackxml' '$output'
+#end if
+  ]]></command>
+    <inputs>
+        <param
+                    label="Collection of files specially named to become tracks"
+                    name="jbrowseme"
+                    type="data_collection">
+        </param>
+        <param type="hidden" name="uglyTestingHack" value="" />
+    </inputs>
+    <outputs>
+        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier"/>
+    </outputs>
+
+    <help><![CDATA[
+
+JBrowse2-in-Galaxy
+==================
+
+JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
+alternative to JBrowse1-in-Galaxy and Trackster.
+
+Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
+and detailed track styling is not yet implemented. Send code.
+JBrowse1 development has now ceased in favour of JBrowse2.
+
+Use and local viewing
+=====================
+
+
+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
+--------
+
+JBrowse is a fast, embeddable genome browser built completely with
+JavaScript and HTML5.
+
+The JBrowse-in-Galaxy (JiG) tool was written to help build complex
+JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
+about how to run the command line tools to format your data, and which
+options need to be supplied and where.
+
+The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
+<https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
+It is maintained by https://github.com/fubar2 who you can help you
+with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
+and disturbed by the distinctly coercive approach to introducing new code,
+compared to the more usual method of providing a working PR.
+
+Options
+-------
+
+**Reference or Assembly**
+
+Choose either a built-in or select one from your history.
+
+Track coordinates and contig names *must* match this reference precisely
+or they will not display.
+
+**Track Groups** represent a set of tracks in a single category.
+
+Annotation Tracks
+-----------------
+
+GFF3/BED
+~~~~~~~~
+
+Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
+
+When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
+to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
+selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
+well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
+lengths of each assembly or reference contig.
+
+BAM Pileups
+~~~~~~~~~~~
+
+We support BAM files and can automatically generate SNP tracks based on
+that bam data.
+
+
+BlastXML
+~~~~~~~~
+
+JiG now supports both blastn and blastp datasets. JiG internally uses a
+blastXML to gapped GFF3 tool to convert your blastxml datasets into a
+format amenable to visualization in JBrowse. This tool is also
+available separately from the IUC on the toolshed.
+
+**Minimum Gap Size** reflects how long a gap must be before it becomes a
+real gap in the processed gff3 file. In the picture above, various sizes
+of gaps can be seen. If the minimum gap size was set much higher, say
+100nt, many of the smaller gaps would disappear, and the features on
+both sides would be merged into one, longer feature. This setting is
+inversely proportional to runtime and output file size. *Do not set this
+to a low value for large datasets*. By setting this number lower, you
+will have extremely large outputs and extremely long runtimes. The
+default was configured based off of the author's experience, but the
+author only works on small viruses. It is *strongly* recommended that
+you filter your blast results before display, e.g. picking out the top
+10 hits or so.
+
+**Protein blast search** option merely informs underlying tools that
+they should adjust feature locations by 3x.
+
+
+@ATTRIBUTION@
+]]></help>
+    <expand macro="citations"/>
+</tool>