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

Uploaded
author fubar
date Fri, 05 Jan 2024 04:31:35 +0000 (12 months ago)
parents 88b9b105c09b
children 6a41f87b5d7f
line wrap: on
line diff
--- a/jbrowse2/jbrowse2.xml	Fri Jan 05 01:58:02 2024 +0000
+++ b/jbrowse2/jbrowse2.xml	Fri Jan 05 04:31:35 2024 +0000
@@ -21,16 +21,11 @@
 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' '$output'
-#end if
+cp '$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":
@@ -212,14 +207,6 @@
             </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"
@@ -230,12 +217,12 @@
             <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>
+                        <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" />
@@ -316,13 +303,12 @@
         <param type="hidden" name="uglyTestingHack" value="" />
     </inputs>
     <outputs>
-        <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier - $standalone"/>
+        <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="standalone" value="minimal" />
             <param name="uglyTestingHack" value="enabled" />
             <output name="output">
                 <assert_contents>
@@ -337,7 +323,6 @@
             <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">
@@ -364,7 +349,6 @@
                  <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">
@@ -388,7 +372,6 @@
         <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>
@@ -410,6 +393,19 @@
 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
 --------
@@ -436,9 +432,7 @@
 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.
+(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
@@ -449,25 +443,14 @@
 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.
+These are standard feature tracks. They usually highlight genes,
+mRNAs and other features of interest along a genomic region.
 
 BAM Pileups
 ~~~~~~~~~~~
@@ -475,11 +458,6 @@
 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
 ~~~~~~~~
@@ -512,12 +490,7 @@
 
 .. 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
 ~~~~~~~~~