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view jbrowse2/jbrowse2.xml @ 10:0db895a99532 draft default tip
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| author | fubar |
|---|---|
| date | Fri, 05 Jan 2024 22:26:16 +0000 |
| parents | 6a41f87b5d7f |
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<tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@" profile="22.05"> <description>genome browser</description> <macros> <import>macros.xml</import> </macros> <expand macro="edamInc"/> <xrefs> <xref type="bio.tools">jbrowse2</xref> </xrefs> <expand macro="requirements"/> <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> <command detect_errors="aggressive"><![CDATA[ mkdir -p '$output.files_path' && ## Copy the XML file into the directory, mostly for debugging ## but nice if users want to reproduce locally cp '$trackxml' '$output.files_path/galaxy.xml' && export JBROWSE_SOURCE_DIR=\$(dirname \$(which jbrowse)) && ## 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' --xml '$trackxml' && cp '$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 ]]></command> <configfiles> <configfile name="dummyIndex"><![CDATA[ <html> <head> </head> <body> <h1>JBrowse2 Data Directory</h1> <p> Hi! This is not a full JBrowse2 instance. JBrowse v0.4(+?) started shipping with the ability to produce just the "data" directory from a JBrowse instance, rather than a complete, standalone instance. This was intended to be used with the in-development Apollo integration, but may have other uses as well. </p> </body> </html> ]]></configfile> <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> <root> <metadata> <genomes> #if str($reference_genome.genome_type_select) == "indexed": <genome path="${reference_genome.genome.fields.path}"> <metadata> <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" size="${dataset.get_size(nice_size=True)}" edam_format="${dataset.datatype.edam_format}" file_ext="${dataset.ext}" /> </metadata> </genome> #else: <genome path="$reference_genome.genome"> <metadata> <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" size="${reference_genome.genome.get_size(nice_size=True)}" edam_format="${reference_genome.genome.datatype.edam_format}" file_ext="${reference_genome.genome.ext}" dname="${reference_genome.genome.element_identifier}" /> <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}" #if $reference_genome.genome.history.user: user_email="${reference_genome.genome.history.user.email}" user_id="${reference_genome.genome.history.user_id}" display_name="${reference_genome.genome.history.get_display_name()}"/> #else user_email="anonymous" user_id="-1" display_name="Unnamed History" /> #end if <metadata #for (key, value) in $reference_genome.genome.get_metadata().items(): #if "_types" not in $key: ${key}="${value}" #end if #end for /> <tool tool_id="${reference_genome.genome.creating_job.tool_id}" tool_version="${reference_genome.genome.creating_job.tool_version}" /> </metadata> </genome> #end if </genomes> <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> </metadata> <tracks> #for $tg in $track_groups: #for $track in $tg.data_tracks: <track cat="${tg.category}" format="${track.data_format.data_format_select}" > #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql": <files> #for $dataset in $track.data_format.annotation: <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> <metadata> <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" size="${dataset.get_size(nice_size=True)}" edam_format="${dataset.datatype.edam_format}" file_ext="${dataset.ext}" /> <history id="${__app__.security.encode_id($dataset.history_id)}" #if $dataset.history.user: user_email="${dataset.history.user.email}" user_id="${dataset.history.user_id}" display_name="${dataset.history.get_display_name()}"/> #else user_email="anonymous" user_id="-1" display_name="Unnamed History"/> #end if <metadata #for (key, value) in $dataset.get_metadata().items(): #if "_types" not in $key and $value is not None and len(str($value)) < 5000: ${key}="${value}" #end if #end for /> <tool tool_id="${dataset.creating_job.tool_id}" tool_version="${dataset.creating_job.tool_version}" /> </metadata> </trackFile> #end for </files> #end if <options> #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" : <style> <className>${track.data_format.jbstyle.style_classname}</className> <description>${track.data_format.jbstyle.style_description}</description> <label>${track.data_format.jbstyle.style_label}</label> <height>${track.data_format.jbstyle.style_height}</height> <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight> </style> #else if str($track.data_format.data_format_select) == "pileup": <pileup> <bam_indices> #for $dataset in $track.data_format.annotation: <bam_index>${dataset.metadata.bam_index}</bam_index> #end for </bam_indices> <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit> </pileup> #end if #if str($track.data_format.data_format_select) == "blast": <blast> #if str($track.data_format.blast_parent) != "": <parent>${track.data_format.blast_parent}</parent> #end if <protein>${track.data_format.is_protein}</protein> <min_gap>${track.data_format.min_gap}</min_gap> <index>${track.data_format.index}</index> </blast> #end if </options> </track> #end for #end for </tracks> <plugins> </plugins> </root> ]]></configfile> </configfiles> <inputs> <conditional name="reference_genome"> <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> <option selected="True" value="indexed">Use a built-in genome</option> <option value="history">Use a genome from history</option> </param> <when value="indexed"> <param help="If your genome of interest is not listed, contact the Galaxy team" label="Select a reference genome" name="genome" type="select"> <options from_data_table="all_fasta"> <filter column="2" type="sort_by"/> <validator message="No genomes are available for the selected input dataset" type="no_options"> </validator> </options> </param> </when> <when value="history"> <param format="fasta" label="Select the reference genome" name="genome" 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"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> <expand macro="track_styling" classname="feature" label="description" description="Hit_titles" height="600px"/> <param label="Features used in Blast Search" help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." format="gff3" name="blast_parent" optional="true" type="data"/> <param label="Minimum Gap Size" help="before a new match_part feature is created" name="min_gap" type="integer" value="10" min="2" /> <param label="Is this a protein blast search?" type="boolean" name="is_protein" truevalue="true" falsevalue="false" /> <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> </when> <when value="vcf"> <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> </when> <when value="gene_calls"> <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> <expand macro="track_styling" classname="feature" label="product,name,id" description="note,description" height="10px"/> <conditional name="match_part" label="match/match_part data"> <param type="select" label="Match part" name="matchp"> <option value="false" selected="True">"No"</option> <option value="true">"Yes"</option> </param> <when value="true"> <param label="Match Part Feature Type" name="name" type="text" value="match" help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)." optional="True"/> </when> <when value="false" /> </conditional> </when> <when value="pileup"> <expand macro="input_conditional" label="BAM Track Data" format="bam" /> <param type="select" label="Autogenerate SNP Track" help="Not recommended for deep coverage BAM files" name="autogen"> <option value="false" selected="True">"No"</option> <option value="true">"Yes"</option> </param> <param label="Maximum size of BAM chunks" name="chunkSizeLimit" type="integer" help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message." value="5000000" /> </when> <when value="wiggle"> <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> </when> </conditional> </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> <has_text text="history id="></has_text> <has_text text="metadata"></has_text> <has_text text="tool_id"></has_text> </assert_contents> </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"/> <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> </conditional> </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="genome path="></has_text> <has_text text="dataset id="></has_text> <has_text text="history id="></has_text> <has_text text="metadata"></has_text> <has_text text="tool_id"></has_text> <has_text text="ext="bed" label="test-3.bed""></has_text> </assert_contents> </output> </test> <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"/> <param name="annotation" value="bam/merlin-sample.bam"/> </conditional> </repeat> </repeat> <param name="uglyTestingHack" value="enabled" /> <output name="output"> <assert_contents> <has_text text="merlin-sample.bam"/> <has_text text="dname="merlin.fa""/> <has_text text="bam_index"/> </assert_contents> </output> </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> </output> </test> </tests> <help><![CDATA[ JBrowse2-in-Galaxy ================== JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible alternative to JBrowse1-in-Galaxy and Trackster. 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. Unzip the archive (*unzip [filename].zip*) and change to the first level directory. It contains 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 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 `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 **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 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 amenable 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. Bigwig XY ~~~~~~~~~ .. image:: bigwig.png VCFs/SNPs ~~~~~~~~~ These tracks do not support any special configuration. @ATTRIBUTION@ ]]></help> <expand macro="citations"/> </tool>