--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse2.xml	Thu Oct 02 10:19:44 2025 +0000
@@ -0,0 +1,1077 @@
+<tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.0">
+    <description>genome browser</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3307</edam_topic>
+        <edam_topic>topic_0092</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_0573</edam_operation>
+        <edam_operation>operation_0564</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">jbrowse_2</xref>
+    </xrefs>
+    <expand macro="requirements"/>
+    <command><![CDATA[
+mkdir -p '$output.files_path/data';
+
+#if $action.action_select == "update":
+    cp -R '$action.update_jbrowse.extra_files_path/data' '$output.files_path/';
+#end if
+
+## Copy the XML file into the directory, mostly for debugging
+## but nice if users want to reproduce locally
+cp '$trackxml' '$output.files_path/galaxy.xml';
+
+export JBROWSE2_SOURCE_DIR=\$(dirname \$(which jbrowse))/../opt/jbrowse2;
+
+## Once that's done, we run the python script to handle the real work
+python '$__tool_directory__/jbrowse2.py'
+--jbrowse \${JBROWSE2_SOURCE_DIR}
+
+#if $action.action_select == "update":
+--update
+#end if
+
+--outdir '$output.files_path'
+'$trackxml';
+
+cp '$output.files_path/index.html' '$output';
+  ]]></command>
+  <configfiles>
+      <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
+#import json
+<root>
+    <metadata>
+        <general>
+            <analytics>${jbgen.enableAnalytics}</analytics>
+            <primary_color>${jbgen.primary_color}</primary_color>
+            <secondary_color>${jbgen.secondary_color}</secondary_color>
+            <tertiary_color>${jbgen.tertiary_color}</tertiary_color>
+            <quaternary_color>${jbgen.quaternary_color}</quaternary_color>
+            <font_size>${jbgen.font_size}</font_size>
+        </general>
+        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
+    </metadata>
+    #for $assembly in $assemblies:
+    <assembly>
+        #if str($assembly.reference_genome.genome_type_select) == "indexed":
+            <genome path="${assembly.reference_genome.genomes.fields.path}" label="${assembly.reference_genome.genomes.fields.name}">
+                <metadata />
+            </genome>
+        #else if str($assembly.reference_genome.genome_type_select) == "remote":
+            <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.label}" remote="true">
+                <metadata />
+            </genome>
+        #else
+            <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.element_identifier}">
+            <metadata>
+                <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" hid="${assembly.reference_genome.genome.hid}"
+                    size="${assembly.reference_genome.genome.get_size(nice_size=True)}"
+                    edam_format="${assembly.reference_genome.genome.datatype.edam_format}"
+                    file_ext="${assembly.reference_genome.genome.ext}"
+                    dname = "${assembly.reference_genome.genome.element_identifier}" />
+                <history id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}"
+                    #if $assembly.reference_genome.genome.history.user:
+                    user_email="${assembly.reference_genome.genome.history.user.email}"
+                    user_id="${assembly.reference_genome.genome.history.user_id}"
+                    display_name="${assembly.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 $assembly.reference_genome.genome.get_metadata().items():
+                    #if "_types" not in $key:
+                    #if isinstance($value, list):
+                        #set value_str = "[%s]" % ','.join([str(val) for val in value])
+                        ${key}="$value_str"
+                    #else
+                        ${key}="${value}"
+                    #end if
+                    #end if
+                    #end for
+                    />
+                <tool
+                    tool_id="${assembly.reference_genome.genome.creating_job.tool_id}"
+                    tool_version="${assembly.reference_genome.genome.creating_job.tool_version}"
+                    />
+            </metadata>
+            #if $assembly.ref_name_aliases:
+                <ref_name_aliases path="${assembly.ref_name_aliases}" />
+            #end if
+            #if $assembly.cytobands:
+                <cytobands path="${assembly.cytobands}" />
+            #end if
+            </genome>
+        #end if
+        <defaultLocation>${assembly.defaultLocation}</defaultLocation>
+    <tracks>
+        #for $tg in $assembly.track_groups:
+        #for $track in $tg.data_tracks:
+        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
+            #if $track.data_format.data_format_select not in ("sparql", "gc"):
+
+                #if $track.data_format.annotation_cond.annotation_source == "history":
+
+                    #if not isinstance($track.data_format.annotation_cond.annotation, list):
+                        ## Synteny tracks allow only one file
+                        #set $annotations = [$track.data_format.annotation_cond.annotation]
+                    #else
+                        #set $annotations = $track.data_format.annotation_cond.annotation
+                    #end if
+                    <files>
+                    #for $dataset in $annotations:
+                    <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
+                        <metadata>
+                        #if $track.data_format.metadata.galaxy_metadata:
+                        <dataset id="${__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:
+                            #if isinstance($value, list) or isinstance($value, dict):
+                                #set value_str = json.dumps(value).replace('"', "&quot;")
+                                ${key}="${value_str}"
+                            #else
+                                ${key}="${value}"
+                            #end if
+                            #end if
+                            #end for
+                            />
+                        <tool
+                            tool_id="${dataset.creating_job.tool_id}"
+                            tool_version="${dataset.creating_job.tool_version}"
+                            />
+                        #end if
+                        #if $track.data_format.metadata.metadata_bonus:
+                            <bonus src="${track.data_format.metadata.metadata_bonus}" />
+                        #end if
+                        </metadata>
+                    </trackFile>
+                    #end for
+                    </files>
+                #else
+
+                    #set $annotations = $track.data_format.annotation_cond.uri
+                    <files>
+                    <trackFile path="${track.data_format.annotation_cond.uri}" ext="${track.data_format.annotation_cond.format}" label="${track.data_format.annotation_cond.label}" remote="true">
+                        <metadata>
+                        #if $track.data_format.metadata.metadata_bonus:
+                            <bonus src="${track.data_format.metadata.metadata_bonus}" />
+                        #end if
+                        </metadata>
+                    </trackFile>
+                    </files>
+                #end if
+            #end if
+
+            <options>
+                <style>
+                    #if str($track.data_format.data_format_select) in ("gene_calls", "pileup", "cram", "wiggle", "vcf", "synteny"):
+                        <display>${track.data_format.jbstyle.track_style.display}</display>
+                    #else if str($track.data_format.data_format_select) in ("hic", "gc", "maf"):
+                        <display>${track.data_format.track_display}</display>
+                    #end if
+
+                    #if str($track.data_format.data_format_select) in ("gene_calls"):
+                        #if str($track.data_format.jbstyle.track_style.display) == "LinearBasicDisplay":
+                            <show_labels type="boolean">${track.data_format.jbstyle.track_style.show_labels}</show_labels>
+                            <show_descriptions type="boolean">${track.data_format.jbstyle.track_style.show_descriptions}</show_descriptions>
+                            <labels_name>${track.data_format.jbstyle.track_style.labels_name}</labels_name>
+                            <descriptions_name>${track.data_format.jbstyle.track_style.descriptions_name}</descriptions_name>
+                            <display_mode>${track.data_format.jbstyle.track_style.display_mode}</display_mode>
+                            <max_height type="integer">${track.data_format.jbstyle.track_style.max_height}</max_height>
+                        #else if str($track.data_format.jbstyle.track_style.display) == "LinearArcDisplay":
+                            <labels_name>${track.data_format.jbstyle.track_style.labels_name}</labels_name>
+                            <display_mode>${track.data_format.jbstyle.track_style.display_mode}</display_mode>
+                        #end if
+                    #end if
+
+                    #if str($track.data_format.data_format_select) in ("pileup", "cram"):
+                        #if str($track.data_format.jbstyle.track_style.display) == "LinearSNPCoverageDisplay":
+                            <scale_type>${track.data_format.jbstyle.track_style.scale_type}</scale_type>
+                            #if str($track.data_format.jbstyle.track_style.min_score) != "":
+                                <min_score type="integer">${track.data_format.jbstyle.track_style.min_score}</min_score>
+                            #end if
+                            #if str($track.data_format.jbstyle.track_style.max_score) != "":
+                                <max_score type="integer">${track.data_format.jbstyle.track_style.max_score}</max_score>
+                            #end if
+                        #end if
+                    #end if
+
+                    #if str($track.data_format.data_format_select) in ("wiggle"):
+                        <renderer>${track.data_format.jbstyle.track_style.wig_renderer}</renderer>
+                    #end if
+                </style>
+
+                #if str($track.data_format.data_format_select) in ("gene_calls"):
+                    <formatdetails>
+                        #if str($track.data_format.formatdetails.formatdetails_feature) != "":
+                        <feature>${track.data_format.formatdetails.formatdetails_feature}</feature>
+                        #end if
+                        #if str($track.data_format.formatdetails.formatdetails_subfeature) != "":
+                        <subfeature>${track.data_format.formatdetails.formatdetails_subfeature}</subfeature>
+                        #end if
+                        #if str($track.data_format.formatdetails.formatdetails_depth) != "":
+                        <depth>${track.data_format.formatdetails.formatdetails_depth}</depth>
+                        #end if
+                    </formatdetails>
+                #end if
+
+                #if str($track.data_format.data_format_select) in ("wiggle"):
+                    #if str($track.data_format.jbstyle.track_style.display) == "MultiLinearWiggleDisplay":
+                        <multitrack type="boolean">True</multitrack>
+                    #end if
+                #end if
+
+                #if str($track.data_format.data_format_select) == "pileup":
+                    <pileup>
+                        #if $track.data_format.annotation_cond.annotation_source == "history":
+                            <bam_indices>
+                                #for $dataset in $track.data_format.annotation_cond.annotation:
+                                    <bam_index>${dataset.metadata.bam_index}</bam_index>
+                                #end for
+                            </bam_indices>
+                        #end if
+                    </pileup>
+                #else if str($track.data_format.data_format_select) == "cram":
+                    <cram>
+                        #if $track.data_format.annotation_cond.annotation_source == "history":
+                            <cram_indices>
+                                #for $dataset in $track.data_format.annotation_cond.annotation:
+                                <cram_index>${dataset.metadata.cram_index}</cram_index>
+                                #end for
+                            </cram_indices>
+                        #end if
+                    </cram>
+                #else if str($track.data_format.data_format_select) == "gene_calls":
+                    <gff>
+                    <index>${track.data_format.index}</index>
+                    </gff>
+                #else if str($track.data_format.data_format_select) == "synteny":
+                    <synteny>
+                    </synteny>
+                #else if str($track.data_format.data_format_select) == "hic":
+                    <hic>
+                    </hic>
+                #else if str($track.data_format.data_format_select) == "maf":
+                    <maf>
+                    <assembly_name>${track.data_format.assembly_name}</assembly_name>
+                    </maf>
+                #else if str($track.data_format.data_format_select) == "sparql":
+                    <label>${track.data_format.label}</label>
+                    <sparql>
+                        <url>${track.data_format.url}</url>
+                        <query>${track.data_format.query}</query>
+                        <query_refnames>${track.data_format.query_refnames}</query_refnames>
+                    </sparql>
+                #else if str($track.data_format.data_format_select) == "wiggle":
+                    <wiggle>
+                    </wiggle>
+                #else if str($track.data_format.data_format_select) == "gc":
+                    <label>GC Content</label>
+                #end if
+            </options>
+        </track>
+        #end for
+        #end for
+    </tracks>
+    </assembly>
+    #end for
+</root>
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="action">
+            <param type="select" label="Action" name="action_select">
+                <option value="create">New JBrowse Instance</option>
+                <option value="update">Update exising JBrowse Instance</option>
+            </param>
+            <when value="create" />
+            <when value="update">
+                <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
+            </when>
+        </conditional>
+
+        <repeat name="assemblies" min="1" title="Genome Assemblies">
+        <conditional name="reference_genome">
+            <param 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>
+                <option value="remote">Use a genome from a remote source (not recommended)</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="genomes"
+                    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" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param
+                    format="fasta"
+                    label="Select the reference genome"
+                    name="genome"
+                    type="data" />
+            </when>
+            <when value="remote">
+                <param name="label" type="text" label="Display name of the genome"/>
+                <param name="uri" type="text" label="URI pointing to a bgzip compressed fasta (.fai and .gzi files expected to be present)"
+                    help="⚠️ WARNING: If this URI is not available for any reason, your JBrowse dataset will be unusable." />
+            </when>
+        </conditional>
+
+        <!-- TODO genetic code not yet supported in jbrowse2
+             https://github.com/GMOD/jbrowse-components/issues/1765
+        -->
+
+        <param label="Default region to display" type="text" name="defaultLocation" value="" help="e.g. 'ctgA:1234..5678'"/>
+
+        <param name="ref_name_aliases" type="data" format="tsv,tabular" label="Reference sequence name aliases" help="Use when chromosomes have alternate names (TSV file: first column is the names from your genome sequence, the rest of the columns are aliases." optional="true" />
+
+        <param name="cytobands" type="data" format="bed" label="cytobands data" help="BED file containing cytobands locations" optional="true" />
+
+        <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"/>
+            <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="gene_calls">GFF/GFF3/BED Features</option>
+                        <option value="pileup">BAM Pileups</option>
+                        <option value="cram">CRAM</option>
+                        <option value="wiggle">BigWig</option>
+                        <option value="vcf">VCF SNPs</option>
+                        <option value="hic">HiC</option>
+                        <option value="maf">MAF</option>
+                        <option value="synteny">Synteny</option>
+                        <option value="sparql">SPARQL</option>
+                        <option value="gc">GC content</option>
+                    </param>
+                    <when value="gene_calls">
+                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
+
+                        <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
+
+                        <expand macro="track_styling_feature"/>
+                        <expand macro="details_panel" />
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="pileup">
+                        <expand macro="input_conditional" label="BAM Track Data" format="bam" />
+                        <expand macro="track_styling_xam"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="cram">
+                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
+                        <expand macro="track_styling_xam"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="wiggle">
+                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
+                        <expand macro="track_styling_bigwig"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="vcf">
+                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
+                        <expand macro="track_styling_vcf"/>
+                        <expand macro="details_panel" />
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="hic">
+                        <expand macro="input_conditional" label="HiC data" format="hic" help="Cool files can be converted to hic format with hictk tool" />
+                        <expand macro="track_styling_hic"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="maf">
+                        <expand macro="input_conditional_no_remote" label="MAF Track Data" format="maf" />
+                        <param name="assembly_name" type="text" label="Assembly name" optional="True" help="As used when creating the MAF file (default: guessed from selected genome assembly)" />
+                        <expand macro="track_styling_maf"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="synteny">
+                        <expand macro="input_conditional" label="PAF Alignment Data" format="paf" multiple="False" help="Query is current assembly, and target is the next assembly. You should not fill this field on the last assembly." />
+                        <expand macro="track_styling_synteny"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                    <when value="sparql">
+                        <!-- Not totally sure it works in real life, probably very rare use case -->
+                        <param type="text" label="SPARQL Server URL" name="url" />
+                        <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
+                        <param type="text" label="SPARQL Query" name="query" area="true">
+                            <sanitizer>
+                                <mapping initial="galaxy.util.mapped_chars">
+                                <add source="&#10;" target=" " />
+                                <add source="&gt;" target="__gt__" />
+                                <add source="&lt;" target="__lt__" />
+                                </mapping>
+                                <valid initial="default">
+                                <add value="|" />
+                                <add value="#" />
+                                <add value="{"/>
+                                <add value="}"/>
+                                <add value="!"/>
+                                <add value="?"/>
+                                <add value="&amp;"/>
+                                <add value="+"/>
+                                <add value="="/>
+                                <add value="'"/>
+                                <add value='"'/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                        <param type="text" label="SPARQL reference names query" help="This query should return a line for each reference name in a `refName` column" name="query_refnames" area="true">
+                            <sanitizer>
+                                <mapping initial="galaxy.util.mapped_chars">
+                                <add source="&#10;" target=" " />
+                                <add source="&gt;" target="__gt__" />
+                                <add source="&lt;" target="__lt__" />
+                                </mapping>
+                                <valid initial="default">
+                                <add value="|" />
+                                <add value="#" />
+                                <add value="{"/>
+                                <add value="}"/>
+                                <add value="!"/>
+                                <add value="?"/>
+                                <add value="&amp;"/>
+                                <add value="+"/>
+                                <add value="="/>
+                                <add value="'"/>
+                                <add value='"'/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                        <expand macro="track_visibility" />
+                    </when>
+
+                    <when value="gc">
+                        <expand macro="track_styling_gc"/>
+                        <expand macro="track_metadata" />
+                        <expand macro="track_visibility" />
+                    </when>
+                </conditional>
+            </repeat>
+        </repeat>
+        </repeat>
+        <expand macro="general_options" />
+    </inputs>
+    <outputs>
+        <data format="html" name="output" label="JBrowse2 on $on_string"/>
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlin.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="gff3/merlin.gff" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="pileup" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bam/merlin-sample.bam" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bw/data.bw"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+                <repeat name="track_groups">
+                    <param name="category" value="Second category" />
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="cram" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="cram/merlin-sample.cram" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bw/data.bw,bw/smaller2.bw"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="vcf" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="vcf/test.vcf" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="hic" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="hic/merlin.hic" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="maf" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="maf/merlinlastz.maf" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gc" />
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/01_all_tracks/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/01_all_tracks/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- Remote data -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="remote"/>
+                    <param name="uri" value="https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz"/>
+                    <param name="label" value="hg19"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" />
+                                <param name="label" value="SKBR3 pacbio coverage (NGMLR)" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw" />
+                                <param name="label" value="SKBR3 pacbio coverage (NGMLR)" />
+                            </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="MultiLinearWiggleDisplay" />
+                                </conditional>
+                            </section>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="pileup" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam" />
+                                <param name="label" value="NA12878 Exome" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="cram" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram" />
+                                <param name="label" value="hg_isoforms.fasta_cram" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="hic" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic" />
+                                <param name="label" value="hg_isoforms.fasta_cram" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="vcf" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz" />
+                                <param name="label" value="HG002 dbVar variant calls" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="vcf" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf" />
+                                <param name="label" value="truthset_somaticSVs_COLO829" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz" />
+                                <param name="label" value="Gencode v36 (GRCh37 liftover)" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz" />
+                                <param name="label" value="wgEncodeDukeMapabilityRegionsExcludable" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/02_remote/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/02_remote/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- Synteny merlin -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlun.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlun_on_merlon.paf"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlon.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlon_on_merlin.paf"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlin.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bw/data.bw"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/03_synteny/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/03_synteny/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- Synteny with remote genomes -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="remote"/>
+                    <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz"/>
+                    <param name="label" value="Peach"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/peach-grape-map.paf"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="remote"/>
+                    <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz"/>
+                    <param name="label" value="Grape"/>
+                </conditional>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/04_synteny_remote/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/04_synteny_remote/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- Synteny with remote genomes *and* paf -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="remote"/>
+                    <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/peach/Ppersica_298_v2.0.fa.gz"/>
+                    <param name="label" value="Peach"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="remote" />
+                                <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/synteny/peach_grape.paf.gz" />
+                                <param name="label" value="Peach vs grape" />
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="remote"/>
+                    <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/grape/Vvinifera_145_Genoscope.12X.fa.gz"/>
+                    <param name="label" value="Grape"/>
+                </conditional>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/05_synteny_full_remote/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/05_synteny_full_remote/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- various options,  cytobands, ref name aliases -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlin.fa"/>
+                </conditional>
+                <param name="ref_name_aliases" value="aliases.tsv"/>
+                <param name="cytobands" value="cytobands.bed"/>
+                <param name="defaultLocation" value="Merlin:1000..2000"/>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="gff3/merlin.gff" />
+                            </conditional>
+                            <param name="index" value="true" />
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearBasicDisplay" />
+                                    <param name="display_mode" value="reducedRepresentation" />
+                                    <param name="labels_name" value="jexl:get(feature,'id')" />
+                                </conditional>
+                            </section>
+                            <section name="metadata">
+                                <param name="galaxy_metadata" value="false" />
+                                <param name="metadata_bonus" value="metadata.tsv" />
+                            </section>
+                            <section name="formatdetails">
+                                <param name="formatdetails_feature" value="jexl:{newfield:'Top custom contents here: '+feature.name}"/>
+                                <param name="formatdetails_subfeature" value="jexl:{newfield:'Sub custom contents here: '+feature.name}"/>
+                                <param name="formatdetails_depth" value="2"/>
+                            </section>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="gene_calls" />
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="gff3/1.gff" />
+                            </conditional>
+                            <param name="index" value="true" />
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearArcDisplay" />
+                                    <param name="display_mode" value="semicircles" />
+                                </conditional>
+                            </section>
+                            <param name="track_visibility" value="default_off" />
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <section name="jbgen">
+                <param name="enableAnalytics" value="true" />
+                <param name="primary_color" value="#9d233f"/>
+                <param name="secondary_color" value="#421e63"/>
+                <param name="tertiary_color" value="#935560"/>
+                <param name="quaternary_color" value="#9fb11d"/>
+                <param name="font_size" value="15" />
+            </section>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/06_various_options/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/06_various_options/config.json" compare="sim_size" />
+            </output>
+        </test>
+        <test> <!-- Synteny, mixed basic / viewer -->
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlun.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlun_on_merlon.paf"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlun_on_merlon.paf"/>
+                            </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearBasicDisplay" />
+                                </conditional>
+                            </section>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlon.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlon_on_merlin.paf"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="synteny"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="paf/merlon_on_merlin.paf"/>
+                            </conditional>
+                            <section name="jbstyle">
+                                <conditional name="track_style">
+                                    <param name="display" value="LinearBasicDisplay" />
+                                </conditional>
+                            </section>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <repeat name="assemblies">
+                <conditional name="reference_genome">
+                    <param name="genome_type_select" value="history"/>
+                    <param name="genome" value="merlin.fa"/>
+                </conditional>
+                <repeat name="track_groups">
+                    <repeat name="data_tracks">
+                        <conditional name="data_format">
+                            <param name="data_format_select" value="wiggle"/>
+                            <conditional name="annotation_cond">
+                                <param name="annotation_source" value="history" />
+                                <param name="annotation" value="bw/data.bw"/>
+                            </conditional>
+                        </conditional>
+                    </repeat>
+                </repeat>
+            </repeat>
+            <output name="output">
+                <extra_files name="galaxy.xml" type="file" value="out/07_synteny_mixed/galaxy.xml" compare="sim_size" />
+                <extra_files name="config.json" type="file" value="out/07_synteny_mixed/config.json" compare="sim_size" />
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+# JBrowse2
+
+JBrowse2 (or simply JBrowse) is a fast, embeddable genome browser built completely with
+JavaScript and HTML5.
+
+The JBrowse2 Galaxy tool was written to help build complex
+JBrowse installations straight from Galaxy, taking advantage of the
+latest Galaxy features such as dataset collections and sections.
+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.
+
+With this tool, you can easily generate a standalone JBrowse browser,
+that you can download, share with collaborators or even publish publicly.
+You can even deposit it as an archive on data repositories for long term
+archival and reuse.
+
+## Options
+
+### Action
+
+The default action of this tool is to create a new JBrowse dataset from scratch.
+However, you have the possibility to add new data (genomes and tracks) to a JBrowse2
+dataset previously generated with the same tool. Note however that mixing synteny and
+non-synteny dataset can give unwanted results.
+
+### Genome assemblies
+
+In JBrowse2 you can as many genome assemblies as needed, each one having its specific
+set of tracks.
+
+To add an assembly, you will need to input its sequence, either from a FASTA file in your history
+or from a genome pre-installed by your server administrators.
+
+### Track Groups
+
+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
+
+Within Track Groups, you have one or more **Annotation Tracks**. Each
+Annotation Track is a dataset, or a group of datasets which have similar styling.
+This allows you to rapidly build up JBrowse instances without having to
+configure tracks individually. 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.
+
+For each track, or group of tracks, you will need to select the corresponding data type
+(GFF, BED, VCF, BAM, CRAM, ...) and the corresponding input files. Depending on the selected
+track type, you will get access to advanced configuration sections where you will be able to
+change the styling of the track. Please consult the [JBrowse2 documentation](https://jbrowse.org/jb2/docs/)
+for more details on all the possibilities. These options will only change the default styling
+of your JBrowse dataset: when visualising it, you will be able to use the JBrowse menus to switch to different
+styling.
+
+When clicking on features in JBrowse (like genes from a GFF), JBrowse opens a panel with detailed
+information about this feature. This panel can also be customized directly from this Galaxy tool, by
+adding new fields, or modifying/removing existing ones.
+
+On different type of tracks, you also have the possiblity to customize metadata associated to tracks.
+Metadata is used by JBrowse to easily sort track in its Faceted Track Selector.
+
+## Special data
+
+### Synteny
+
+JBrowse2 allows to display synteny relationships between different genomes. To use it with this tool,
+generate alignement data between your different genomes (with minimap2 for example), then add the different genomes
+one by one, and a synteny track to the each genome corresponding to alignements to the
+next one.
+
+For example, say you have 3 genomes : A, B and C
+- align genome B on genome A, and genome C on genome B
+- add genome C, B, and A in the Galaxy tool
+- add a synteny track on genome C where you input the alignement against genome B
+- add a synteny track on genome B where you input the alignement against genome A
+
+Multiway synteny representation is not yet possible.
+
+### Remote data sources
+
+We have made the choice to allow selecting data from remote sources (HTTP) instead of datasets from your history.
+Please be **very careful** when using this feature: by using it, your dataset will no longer be standalone, it will
+depend on the existence of the remote data. If for any reason the remote server administrator decides to remove or change
+the access rights to the corresponding file, your JBrowse dataset will become unusable.
+
+Using remote data sources can be useful when using this tool for specific projects with associated reliable data
+repositories, but for most other use cases, selecting datasets from history is much more recommended.
+]]></help>
+    <expand macro="citations"/>
+</tool>