comparison jbrowse2.xml @ 17:4c201a3d4755 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66

16:1fe91657bfd6

 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_1" profile="22.05">
    <description>genome browser</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edamInc"/>

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 is maintained by `the Galaxy IUC
<https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you
with missing features or bugs in the tool.

Options
-------

The first option you encounter is the **Reference sequence(s)** to use. This option
now accepts multiple fasta files, allowing you to build JBrowse2
instances that contain data for multiple genomes or chrosomomes
(generally known as "landmark features" in gff3 terminology.)

**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.

Annotation Tracks
-----------------

There are a few different types of tracks supported, each with their own
set of options:

GFF3/BED
~~~~~~~~

These are 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.

BAM Pileups
~~~~~~~~~~~

We support BAM files and can automatically generate SNP tracks based on

17:4c201a3d4755

 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@.1" profile="22.05">
    <description>genome browser</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edamInc"/>

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