comparison jbrowse2/jbrowse2.xml @ 7:234cf4490901 draft

Uploaded

6:88b9b105c09b

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse2.py'

--jbrowse \${JBROWSE_SOURCE_DIR}
--standalone '$standalone'

--outdir '$output.files_path'
'$trackxml' &&

#if str($standalone) != "data":
    cp '$output.files_path/index.html' '$output'
#else:
    cp '$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'
#end if

                    type="data">
                </param>
            </when>
        </conditional>

        <param name="standalone" label="Include all reference and track data in the JBrowse2 object" type="select"
              help="Default is efficient but will not work offline. Including reference sequences, tracks and indexes will allow standalone viewing, at the cost of copying and moving all data" >
            <option value="complete">Complete: Choose ONLY if need to view offline, or if history cannot be published. WARNING: produces bloated downloads storing redundant copies of all data!
            </option>
            <option value="minimal" selected="true">Sufficient: Uses URLs for Galaxy data. Requires internet access and a published history to download, share and view remotely.
            </option>
        </param>

        <repeat name="track_groups" title="Track Group">
            <param label="Track Category"
                name="category"
                type="text"
                value="Default"
                help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False">
             </param>
            <repeat name="data_tracks" title="Annotation Track">
                <conditional name="data_format" label="Track Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="blast">Blast XML</option>
                        <option value="gene_calls">GFF/GFF3/BED Features</option>
                        <option value="hic">HiC data (convert .cool with hicexplorer)</option>
                        <option value="pileup">BAM Pileups</option>
                        <option value="vcf">VCF SNPs</option>
                        <option value="wiggle">BigWig XY</option>
                    </param>
                    <when value="hic">
                        <expand macro="input_conditional" label="HiC Track Data" format="hic" help="Cool files must be converted first with hicexplorer" />
                    </when>
                    <when value="blast">

            </repeat>
        </repeat>
        <param type="hidden" name="uglyTestingHack" value="" />
    </inputs>
    <outputs>
        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier - $standalone"/>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
                <param name="standalone" value="minimal" />
            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="genome path="></has_text>
                    <has_text text="dataset id="></has_text>

            </output>
            </test>
            <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <param name="standalone" value="minimal" />
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>

        <test>
            <conditional name="reference_genome">
                 <param name="genome_type_select" value="history"/>
                 <param name="genome" value="merlin.fa"/>
            </conditional>
            <param name="standalone" value="minimal" />
            <repeat name="track_groups">
                <param name="category" value="Auto Coloured" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="pileup"/>

        </test>

        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <param name="standalone" value="minimal" />
            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="merlin.fa"/>
                </assert_contents>

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.


Overview
--------

JBrowse is a fast, embeddable genome browser built completely with

-------

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.

**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
~~~~~~~~

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 fail under BED datasets.

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.

BlastXML
~~~~~~~~

.. image:: blast.png

Bigwig XY
~~~~~~~~~

.. image:: bigwig.png

**XYPlot**

BigWig tracks can be displayed as a "density" plot which is a continuous
line which varies in colour, or as an "XYplot." XYplots are preferable
for users to visually identify specific features in a bigwig track,
however density tracks are more visually compact.

VCFs/SNPs
~~~~~~~~~

These tracks do not support any special configuration.

7:234cf4490901

## Once that's done, we run the python script to handle the real work
python '$__tool_directory__/jbrowse2.py'

--jbrowse \${JBROWSE_SOURCE_DIR}

--outdir '$output.files_path'
'$trackxml' &&

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

                    type="data">
                </param>
            </when>
        </conditional>

        <repeat name="track_groups" title="Track Group">
            <param label="Track Category"
                name="category"
                type="text"
                value="Default"
                help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False">
             </param>
            <repeat name="data_tracks" title="Annotation Track">
                <conditional name="data_format" label="Track Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="blast">Blast XML track - converted to GFF with actual gaps between hits</option>
                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature tracks</option>
                        <option value="hic">HiC binary data. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
                        <option value="pileup">BAM Pileup track</option>
                        <option value="vcf">VCF SNP annotation track</option>
                        <option value="wiggle">BigWig XY track</option>
                    </param>
                    <when value="hic">
                        <expand macro="input_conditional" label="HiC Track Data" format="hic" help="Cool files must be converted first with hicexplorer" />
                    </when>
                    <when value="blast">

            </repeat>
        </repeat>
        <param type="hidden" name="uglyTestingHack" value="" />
    </inputs>
    <outputs>
        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier"/>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="genome path="></has_text>
                    <has_text text="dataset id="></has_text>

            </output>
            </test>
            <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>

        <test>
            <conditional name="reference_genome">
                 <param name="genome_type_select" value="history"/>
                 <param name="genome" value="merlin.fa"/>
            </conditional>
            <repeat name="track_groups">
                <param name="category" value="Auto Coloured" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="pileup"/>

        </test>

        <test>
            <param name="reference_genome|genome_type_select" value="history"/>
            <param name="reference_genome|genome" value="merlin.fa"/>
            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="merlin.fa"/>
                </assert_contents>

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).
They can also be downloaded as archives ("floppy disk" icon) to share and for local viewing.
One extra step is required before they can be viewed. A local python web server must be started using a script included in each archive.
Unpack the archive (tar -xvzf [filename].tgz) and the first level directory will contain a file named "servejb2.py"

Assuming you have python3 installed, running

*python3 servjb2.py*

will serve the unarchived JBrowse2 configuration, so it can be browsed by pointing a web browser to localhost:8080

Overview
--------

JBrowse is a fast, embeddable genome browser built completely with

-------

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.)

**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
-----------------

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.

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

We support BAM files and can automatically generate SNP tracks based on
that bam data.


BlastXML
~~~~~~~~

.. image:: blast.png

Bigwig XY
~~~~~~~~~

.. image:: bigwig.png



VCFs/SNPs
~~~~~~~~~

These tracks do not support any special configuration.