--- a/jbrowse.xml	Wed Dec 30 18:09:50 2015 -0500
+++ b/jbrowse.xml	Thu Dec 31 11:51:40 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="0.3">
+<tool id="jbrowse" name="JBrowse" version="0.4">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -23,15 +23,15 @@
 --outdir $output.files_path;
 
 #if str($standalone) == "Complete":
-    cat $output.files_path/index.html > $output;
+    mv $output.files_path/index.html $output;
 #else:
-    cat $dummyIndex > $output;
+    mv $dummyIndex $output;
 #end if
 
 
 ## 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
+    mv $trackxml $output
 #end if
 ]]></command>
   <configfiles>
@@ -339,7 +339,259 @@
       <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
   </outputs>
   <help><![CDATA[
-Build a static JBrowse visualization of a genome and some associated datasets.
+JBrowse-in-Galaxy
+=================
+
+JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
+alternative to Trackster.
+
+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, taking advantage of the
+latest Galaxy features such as dataset collections, sections, and colour
+pickers. 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. Additionally it comes with many
+javascript functions to handle colouring of features which would be
+nearly impossible to write without the assistance of this tool.
+
+The JBrowse-in-Galaxy tool is maintained by `Eric
+Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
+encounter missing features or bugs.
+
+Options
+-------
+
+The first option you encounter is the **Fasta Sequence(s)**. This option
+now accepts multiple fasta files, allowing you to build JBrowse
+instances that contain data for multiple genomes or chrosomomes
+(generally known as "landmark features" in gff3 terminology.) Up to 30
+will be shown from the dropdown selector within JBrowse, this is a known
+issue.
+
+**Standalone Instances** are a somewhat in-development feature.
+Currently Galaxy copies the entire JBrowse directory in order to have a
+complete, downloadable file that contains a ready-to-go JBrowse
+instance. This is obviously an anti-feature because users don't want a
+complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
+dataset in their history, and admins don't want useless copies of
+JBrowse on disk. Unfortunately we have not come up with the perfect
+solution just yet, but we're working on it! In the meantime, users have
+been given the option to produce just the ``data/`` directory. For those
+unfamiliar with JBrowse, the ``data/`` directory contains processed data
+files, but no way to view them. This feature is additionally implemented
+for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
+
+**Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
+which allows users to specify a non standard genetic code, and have
+JBrowse highlight the correct start and stop codons. If you would like
+to use a coding table not provided by this list, please let
+`me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for
+this.
+
+**Track Groups** represent a set of tracks in a single category. These
+can be used to let your users understand relationships between large
+groups of tracks.
+
+.. image:: sections.png
+
+Annotation Tracks
+-----------------
+
+Within Track Groups, you have one or more **Annotation Tracks**. Each
+Annotation Track is a groups of datasets which have similar styling.
+This allows you to rapidly build up JBrowse instances without having to
+configure tracks individually. A massive improvement over previous
+versions. For example, if you have five different GFF3 files from
+various gene callers that you wish to display, you can take advantage of
+this feature to style all of them similarly.
+
+There are a few different types of tracks supported, each with their own
+set of options:
+
+GFF3/BED/GBK
+~~~~~~~~~~~~
+
+These are your standard feature tracks. They usually highlight genes,
+mRNAs and other features of interest along a genomic region. The
+underlying tool and this help documentation focus primarily on GFF3
+data, and have not been tested extensively with other formats. Automatic
+min/max detection will likely fail under BED and GBK datasets.
+
+The data may be of a subclass we call **match/match part** data. This
+consists of top level ``match`` features, with a child ``match_part``
+feature, and is often used in displaying alignments. (See "Alignments"
+section on the `GFF3
+specification <http://www.sequenceontology.org/gff3.shtml>`__ for more
+information). If the data is match/match part, you will need to specify
+the top level match feature name, as it can be one of a few different SO
+terms, and JiG does not yet have the ability to understand SO terms.
+
+Next up is the **Styling Options** section, which lets you control a few
+properties on how the track is styled. Most of these you will not need
+to configure and can safely leave on defaults. Occasionally you will
+want to change what information is shown in the end product.
+
+.. image:: styling.png
+
+In the above image you can see some black text, and some blue text. The
+source of the black text is configured with the **style.label** option,
+and the source of the blue text is configured with the
+**style.description** option.
+
+Feature Score Scaling & Colouring Options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+First, you need to choose between ignoring the score attribute of GFF3
+files, or using it. If you choose to ignore it, all features will be
+coloured with a solid colour. If you choose to use it, features will
+have slightly different colours based on their scores.
+
+.. image:: opacity.png
+
+If you choose **Ignore score**, you may choose between automatically
+choosing a colour, or manually specifying one. The automatically chosen
+colours vary along a brewer palette and generally look quite nice with
+no human intervention required. The manual colour choice is somewhat
+self explanatory. Clicking on the small coloured square will bring up a
+colour palette.
+
+If you choose **Base on score**, you're faced with a dizzying array of
+options. First is the function to map the colour choices to colour
+values. JiG comes with a few functions built in such as linear scaling,
+logarithmic scaling, and blast scaling.
+
+The **linear scaling** method says "take these values, and they map
+directly to a range of output values". **Logarithmic scaling** says
+"please take the log of the score before mapping", and **Blast scaling**
+is further specialised to handle blast data more nicely. These are
+convenience functions to help transform the wide array of possible
+values in the GFF3 score attribute to more meaningful numbers. If you
+need more comprehensive score scaling, it is recommended that you
+pre-process your GFF3 files somehow.
+
+Once you've selected a scaling method, you can choose to manually
+specify the minimum and maximum expected values, or you can let JiG
+determine them for you automatically.
+
+Finally, opacity is the only mapping we currently provide. Future
+iterations will attempt to improve upon this and provide more colour
+scales. The Opacity option maps the highest scoring features to full
+opacity, and everything else to lower ones.
+
+BAM Pileups
+~~~~~~~~~~~
+
+We support BAM files and can automatically generate SNP tracks based on
+that bam data.
+
+.. image:: bam.png
+
+This is *strongly discouraged* for high coverage density datasets.
+Unfortunately there are no other configuration options exposed for bam
+files. If you find JBrowse options you wish to see exposed, please let
+`me <mailto:esr+jig@tamu.edu>`__ know.
+
+BlastXML
+~~~~~~~~
+
+.. image:: blast.png
+
+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 ammenable 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.
+
+Styling Options
+^^^^^^^^^^^^^^^
+
+Please see the styling options for GFF3 datasets, they are identical.
+
+Feature Score Scaling & Coloring Options
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Please see the score scaling and colouring options for GFF3 datasets,
+they are identical. Remember to set your score scaling to "blast" method
+if you do use it.
+
+Bigwig XY
+~~~~~~~~~
+
+.. image:: bigwig.png
+
+**XYPlot**
+
+BigWig tracks can be displayed as a "density" plot which is continuous
+line which varies in colour, or as an "XYplot." XYplots are preferrable
+for users to visually identify specific features in a bigwig track,
+however density tracks are more visually compact.
+
+**Variance Band** is an option available to XYPlots, and can be seen in
+the third and fourth tracks in the above picture. This overlays a mean
+line, and 1 and 2 standard deviation areas.
+
+**Track Scaling** is different from colour scaling, instead it
+configures how the track behaves inside of JBrowse. **Autoscaling
+globally** means that JBrowse will determine the minimum and maximum for
+the track, and fix the bounds of the viewport to that. E.g. if your
+track ranges from 1-1000, and the region you're currently zoomed to only
+goes from 0-50, then the viewport range will still show 1-1000. This is
+good for global genomic context. However you may wish to consider
+**autoscaling locally** instead. In the example of a region which varies
+from 0-50, autoscaling locally would cause the individual track's
+viewport to re-adjust and show just the 0-50 region. If neither of these
+options are paletable, you may manually hardcode the minimum and
+maximums for the track to scale to.
+
+Colour Options
+^^^^^^^^^^^^^^
+
+BigWig tracks have two colours in JBrowse, a positive and a negative
+colour.
+
+As always you may manually choose a colour, or let JiG choose for you.
+
+One of the more interesting options is the **Bicolor pivot**. This
+option allows you to control the point at which JBrowse switches from
+the positive colour to the negative. In the above graphic, you can see
+this has been configured to "mean" for the first two (orange and blue)
+tracks.
+
+VCFs/SNPs
+~~~~~~~~~
+
+These tracks do not support any special configuration.
+
+Known Issues
+------------
+
+-  More than 30 landmark features cannot be listed in the manual
+   selector.
+-  Non GFF3 likely has issue with automatically determined min/max
+   scores. Manually specify minimum and maximum score attributes, or do
+   not use varied colours based on scores to avoid this issue.
+
 
 @ATTRIBUTION@
 ]]></help>