comparison jbrowse2.xml @ 112:56f9a6e0fe80 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792

111:0a532764dcfa

    <expand macro="edamInc"/>
    <xrefs>
        <xref type="bio.tools">jbrowse2</xref>
    </xrefs>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <required_files>
        <include path="autogenJB2.py"/>
        <include path="blastxml_to_gapped_gff3.py"/>
        <include path="convertMAF.sh"/>
        <include path="gff3_rebase.py"/>

                </when>
                <when value="uri">
                    <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" 
                        help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
                    </param>
                    <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4">
                    </param>
                </when>
            </conditional>
            <repeat name="track_groups" title="Track Group">
                <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/>
                <repeat name="data_tracks" title="Annotation Track">

Use and local viewing
=====================

Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.

At present, 10 Galaxy datatypes that 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

**Track Groups** represent a set of tracks in a single category.


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

MAF
~~~

For history references, the name of the reference genome dataset in your history is very important for MAF tracks,

112:56f9a6e0fe80

    <expand macro="edamInc"/>
    <xrefs>
        <xref type="bio.tools">jbrowse2</xref>
    </xrefs>
    <expand macro="requirements"/>
    <required_files>
        <include path="autogenJB2.py"/>
        <include path="blastxml_to_gapped_gff3.py"/>
        <include path="convertMAF.sh"/>
        <include path="gff3_rebase.py"/>

                </when>
                <when value="uri">
                    <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" 
                        help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
                    </param>
                    <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/>
                </when>
            </conditional>
            <repeat name="track_groups" title="Track Group">
                <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/>
                <repeat name="data_tracks" title="Annotation Track">

Use and local viewing
=====================

Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.

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

**Track Groups** represent a set of tracks in a single category.


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


BED
~~~

Bed feature annotation usually requires clicking on the feature. 

Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5
set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5 
for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track.


MAF
~~~

For history references, the name of the reference genome dataset in your history is very important for MAF tracks,