comparison jbrowse.xml @ 25:1cfc579079a6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f

24:fa30df9b79c2

  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
  <command><![CDATA[
#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:
    cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
#end if

            #if str($reference_genome.genome_type_select) == "indexed":
              <genome path="${reference_genome.genomes.fields.path}">
                  <metadata />
              </genome>s
            #else
              #for $genome in $reference_genome.genomes:
                  <genome path="$genome">
                    <metadata>
                      <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
                          size="${genome.get_size(nice_size=True)}"
                          edam_format="${genome.datatype.edam_format}"
                          file_ext="${genome.ext}" />
                      <history id="${__app__.security.encode_id($genome.history_id)}"
                          user_email="${genome.history.user.email}"
                          user_id="${genome.history.user_id}"
                          display_name="${genome.history.get_display_name()}"/>
                      <metadata
                          #for (key, value) in $genome.get_metadata().items():
                          #if "_types" not in $key:
                          ${key}="${value}"
                          #end if
                          #end for
                          />
                      <tool
                          tool_id="${genome.creating_job.tool_id}"
                          tool_version="${genome.creating_job.tool_version}"
                          />
                    </metadata>
                  </genome>
              #end for
            #end if
        </genomes>
        <general>
            <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
            <trackPadding>${jbgen.trackPadding}</trackPadding>

        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
    </metadata>
    <tracks>
        #for $tg in $track_groups:
        #for $track in $tg.data_tracks:
        #if $track.data_format.data_format_select == "rest":
        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
            <url>${track.data_format.url}</url>
        </track>
        #else:
        <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
            <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}"

                      />
                </metadata>
              </trackFile>
              #end for
            </files>

            <options>
            #if str($track.data_format.data_format_select) == "gene_calls" or  str($track.data_format.data_format_select) == "blast":
                <style>
                    <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
                    <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
                    <className>${track.data_format.jbstyle.style_classname}</className>
                    <description>${track.data_format.jbstyle.style_description}</description>

                  #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
                    <bicolor_pivot>mean</bicolor_pivot>
                  #else:
                    <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
                  #end if
                </wiggle>
            #else if str($track.data_format.data_format_select) == "pileup":
                <pileup>
                    <auto_snp>${track.data_format.auto_snp}</auto_snp>
                    <bam_indices>
                        #for $dataset in $track.data_format.annotation:
                        <bam_index>${dataset.metadata.bam_index}</bam_index>
                        #end for
                    </bam_indices>
                </pileup>
            #else if str($track.data_format.data_format_select) == "blast":
                <blast>
                  #if str($track.data_format.blast_parent) != "":
                    <parent>${track.data_format.blast_parent}</parent>

                  #if $track.data_format.match_part.match_part_select:
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                    <index>${track.data_format.index}</index>
                </gff>
##            #else if str($track.data_format.data_format_select) == "sparql":
##                <sparql>
##                    <url>${track.data_format.url}</url>
##                    <label>${track.data_format.label}</label>
##                    <!-- This is going to be an absolutey nightmare -->
##                    <query>${track.data_format.query}</query>
##                </sparql>
            #end if
            </options>
        </track>
        #end if
        #end for
        #end for
    </tracks>
    <plugins
        ComboTrackSelector="${plugins.ComboTrackSelector}"
        Bookmarks="${plugins.Bookmarks}"
        GCContent="${plugins.GCContent}"
        theme="${plugins.theme}"
        />
</root>]]></configfile>
  </configfiles>
  <inputs>
    <conditional name="reference_genome">

        </when>
        <when value="history">
            <param
              format="fasta"
              label="Select the reference genome"
              name="genomes"
              type="data"
              multiple="True" />
        </when>
    </conditional>

    <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>

                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML</option>
                <option value="wiggle">BigWig XY</option>
                <option value="vcf">VCF SNPs</option>
                <option value="rest">REST Endpoint</option>
                <!--<option value="sparql">SPARQL</option>-->
            </param>
            <when value="blast">
                <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                <param label="Features used in Blast Search"

                <conditional name="track_config">
                    <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
                        <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                        <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
                        <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
                    </param>
                    <when value="JBrowse/View/Track/CanvasFeatures">
                        <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
                            <param label="Transcript type"
                                   name="transcriptType"

                                  value=""
                                  help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
                                  optional="True"/>
                      </section>
                  </when>
                  <when value="BlastView/View/Track/CanvasFeatures" />
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />

                       help="Not recommended for deep coverage BAM files"
                       type="boolean"
                       name="auto_snp"
                       truevalue="true"
                       falsevalue="false" />
                <expand macro="track_display" />
            </when>
            <when value="wiggle">
                <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />

                </conditional>
                <param type="select" label="Visual Scaling" name="scale_select2">
                    <option value="linear" selected="true">Linear</option>
                    <option value="log">Logarithmic (Dynamically Calculated)</option>
                </param>
                <expand macro="color_selection_minmax" />
                <expand macro="track_display" />
            </when>
            <when value="rest">
                <param type="text" label="REST Endpoint" name="url" />
            </when>
            <!--
            <when value="sparql">
                <param type="text" label="SPARQL Server URL" name="url" />
                <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
                <param type="text" label="SPARQL Query" name="query" area="true" />
                <expand macro="track_display" />
            </when>
            -->
        </conditional>
    </repeat>
    </repeat>

    <expand macro="general_options" />
    <section name="plugins" title="Plugins" expanded="false">
        <param
            label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
            help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
        <param
            label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
            help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />

        <param
            label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
            help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />

        <param type="select" label="JBrowse Theme" name="theme">
            <option value="" selected="True">Default</option>
            <option value="Minimalist">Minimalist</option>
            <option value="Dark">Dark</option>
        </param>
    </section>

    <param type="hidden" name="uglyTestingHack" value="" />
  </inputs>
  <outputs>

  </outputs>
  <tests>
    <test>
      <!-- gencode -->
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genomes" value="merlin.fa"/>
      <param name="gencode" value="1" />
      <param name="standalone" value="Data Directory" />
      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genomes" value="merlin.fa"/>
      <param name="gencode" value="11" />
      <param name="standalone" value="Data Directory" />
      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gencode/test.xml" lines_diff="14"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genomes" value="merlin.fa"/>
      <param name="gencode" value="11" />
      <param name="standalone" value="Data Directory" />
      <repeat name="track_groups">
        <param name="category" value="Auto Coloured" />
        <repeat name="data_tracks">

      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gff3/test.xml" lines_diff="256" />
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genomes" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="With menu or index" />

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="menus/test.xml" lines_diff="24"/>
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genomes" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="With canvas config" />

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="26"/>
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genomes" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="Auto Coloured" />

    </test>

    <test>
        <!-- data_table -->
        <param name="reference_genome|genome_type_select" value="indexed"/>
        <param name="reference_genome|genomes" value="merlin"/>
        <param name="gencode" value="1" />
        <param name="standalone" value="Data Directory" />
        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================

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 `Eric
Rasche <mailto:[e-mail]>`__, who you can contact if you
encounter missing features or bugs.

Options
-------

The first option you encounter is the **Fasta Sequence(s)**. This option

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.

**Standalone Instances** are a somewhat in-development feature.
Currently Galaxy copies the entire JBrowse directory in order to have a
complete, downloadable file that contains a ready-to-go JBrowse
instance. This is obviously an anti-feature because users don't want a
complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
dataset in their history, and admins don't want useless copies of
JBrowse on disk. Unfortunately we have not come up with the perfect
solution just yet, but we're working on it! In the meantime, users have
been given the option to produce just the ``data/`` directory. For those
unfamiliar with JBrowse, the ``data/`` directory contains processed data
files, but no way to view them. This feature is additionally implemented
for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.

**Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
which allows users to specify a non standard genetic code, and have
JBrowse highlight the correct start and stop codons. If you would like
to use a coding table not provided by this list, please let
`me <mailto:[e-mail]>`__ know so that I may add support for
this.

**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:: bam.png

This is *strongly discouraged* for high coverage density datasets.
Unfortunately there are no other configuration options exposed for bam
files. If you find JBrowse options you wish to see exposed, please let
`me <mailto:[e-mail]>`__ know.

BlastXML
~~~~~~~~

.. image:: blast.png

25:1cfc579079a6

  <description>genome browser</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command>
  <command detect_errors="aggressive"><![CDATA[
#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:
    cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
#end if

            #if str($reference_genome.genome_type_select) == "indexed":
              <genome path="${reference_genome.genomes.fields.path}">
                  <metadata />
              </genome>s
            #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="${reference_genome.genome.ext}" />
                  <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}"
                      user_email="${reference_genome.genome.history.user.email}"
                      user_id="${reference_genome.genome.history.user_id}"
                      display_name="${reference_genome.genome.history.get_display_name()}"/>
                  <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>
        <general>
            <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
            <trackPadding>${jbgen.trackPadding}</trackPadding>

        <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="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
            #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}"

                      />
                </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" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql":
                <style>
                    <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
                    <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
                    <className>${track.data_format.jbstyle.style_classname}</className>
                    <description>${track.data_format.jbstyle.style_description}</description>

                  #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
                    <bicolor_pivot>mean</bicolor_pivot>
                  #else:
                    <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
                  #end if
                  <multibigwig>${track.data_format.MultiBigWig}</multibigwig>
                </wiggle>
            #else if str($track.data_format.data_format_select) == "pileup":
                <pileup>
                    <auto_snp>${track.data_format.auto_snp}</auto_snp>
                    <bam_indices>
                        #for $dataset in $track.data_format.annotation:
                        <bam_index>${dataset.metadata.bam_index}</bam_index>
                        #end for
                    </bam_indices>
                    <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit>
                </pileup>
            #else if str($track.data_format.data_format_select) == "blast":
                <blast>
                  #if str($track.data_format.blast_parent) != "":
                    <parent>${track.data_format.blast_parent}</parent>

                  #if $track.data_format.match_part.match_part_select:
                    <match>${track.data_format.match_part.name}</match>
                  #end if
                    <index>${track.data_format.index}</index>
                </gff>
            #else if str($track.data_format.data_format_select) == "rest":
                <label>${track.data_format.label}</label>
                <rest>
                    <url>${track.data_format.url}</url>
                </rest>
            #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>
                </sparql>
            #end if
            </options>
        </track>
        #end for
        #end for
    </tracks>
    ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed
    ## <plugins
    ##     ComboTrackSelector="${plugins.ComboTrackSelector}"
    ##     Bookmarks="${plugins.Bookmarks}"
    ##     GCContent="${plugins.GCContent}"
    ##     BlastView="${plugins.BlastView}"
    ##     theme="${plugins.theme}"
    ##     />
    <plugins
        ComboTrackSelector="${plugins.ComboTrackSelector}"
        Bookmarks=""
        GCContent="${plugins.GCContent}"
        BlastView="${plugins.BlastView}"
        theme=""
        />
</root>]]></configfile>
  </configfiles>
  <inputs>
    <conditional name="reference_genome">

        </when>
        <when value="history">
            <param
              format="fasta"
              label="Select the reference genome"
              name="genome"
              type="data" />
        </when>
    </conditional>

    <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>

                <option value="pileup">BAM Pileups</option>
                <option value="blast">Blast XML</option>
                <option value="wiggle">BigWig XY</option>
                <option value="vcf">VCF SNPs</option>
                <option value="rest">REST Endpoint</option>
                <option value="sparql">SPARQL</option>
            </param>
            <when value="blast">
                <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                <param label="Features used in Blast Search"

                <conditional name="track_config">
                    <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
                        <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                        <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
                        <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
                    </param>
                    <when value="JBrowse/View/Track/CanvasFeatures">
                        <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
                            <param label="Transcript type"
                                   name="transcriptType"

                                  value=""
                                  help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
                                  optional="True"/>
                      </section>
                  </when>
                  <!--when value="BlastView/View/Track/CanvasFeatures" /-->
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />

                       help="Not recommended for deep coverage BAM files"
                       type="boolean"
                       name="auto_snp"
                       truevalue="true"
                       falsevalue="false" />
                <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" />
                <expand macro="track_display" />
            </when>
            <when value="wiggle">
                <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />

                </conditional>
                <param type="select" label="Visual Scaling" name="scale_select2">
                    <option value="linear" selected="true">Linear</option>
                    <option value="log">Logarithmic (Dynamically Calculated)</option>
                </param>

                <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean"
                    help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." />

                <expand macro="color_selection_minmax" />
                <expand macro="track_display" />
            </when>
            <when value="rest">
                <param type="text" label="REST Endpoint" name="url" />
                <param type="text" label="Track Label" name="label" value="REST Genes" />
                <expand macro="track_styling"
                        classname="feature"
                        label="description"
                        description="Hit_titles"
                        height="600px"/>
                <expand macro="color_selection"
                        token_scaling_lin_select="false"
                        token_scaling_log_select="true" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>

            <when value="sparql">
                <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>
                <expand macro="track_styling"
                        classname="feature"
                        label="description"
                        description="Hit_titles"
                        height="600px"/>
                <expand macro="color_selection"
                        token_scaling_lin_select="false"
                        token_scaling_log_select="true" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>
        </conditional>
    </repeat>
    </repeat>

    <expand macro="general_options" />
    <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed -->
    <section name="plugins" title="Plugins" expanded="false">

        <param
            label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true"
            help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." />

        <param
            label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
            help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
        <!-- No way to disable now that it's built in jbrowse conda package -->
        <!--param
            label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
            help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /-->

        <param
            label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
            help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />

        <!--param type="select" label="JBrowse Theme" name="theme">
            <option value="" selected="True">Default</option>
            <option value="Minimalist">Minimalist</option>
            <option value="Dark">Dark</option>
        </param-->
    </section>

    <param type="hidden" name="uglyTestingHack" value="" />
  </inputs>
  <outputs>

  </outputs>
  <tests>
    <test>
      <!-- gencode -->
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genome" value="merlin.fa"/>
      <param name="gencode" value="1" />
      <param name="standalone" value="Data Directory" />
      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genome" value="merlin.fa"/>
      <param name="gencode" value="11" />
      <param name="standalone" value="Data Directory" />
      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gencode/test.xml" lines_diff="14"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genome" value="merlin.fa"/>
      <param name="gencode" value="11" />
      <param name="standalone" value="Data Directory" />
      <repeat name="track_groups">
        <param name="category" value="Auto Coloured" />
        <repeat name="data_tracks">

      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gff3/test.xml" lines_diff="256" />
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="With menu or index" />

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="menus/test.xml" lines_diff="24"/>
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="With canvas config" />

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="26"/>
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="Auto Coloured" />

    </test>

    <test>
        <!-- data_table -->
        <param name="reference_genome|genome_type_select" value="indexed"/>
        <param name="reference_genome|genome" value="merlin"/>
        <param name="gencode" value="1" />
        <param name="standalone" value="Data Directory" />
        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
    </test>

    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" value="merlin.fa"/>
        <param name="gencode" value="11" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="External endpoints" />
            <repeat name="data_tracks">
                <conditional name="data_format">
                    <param name="data_format_select" value="rest"/>
                    <param name="url" value="http://example.org.external/rest_api/"/>
                    <param name="label" value="Rest api"/>
                </conditional>
            </repeat>
            <repeat name="data_tracks">
                <conditional name="data_format">
                    <param name="data_format_select" value="sparql"/>
                    <param name="url" value="http://example.org.external/sparql/"/>
                    <param name="label" value="Sparql endpoint"/>
                    <param name="query" value="  DEFINE sql:select-option 'order'
  prefix rdf:    &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
  select ?start,
         ?end,
         IF( ?faldo_type = faldo:ForwardStrandPosition,
             1,
             IF( ?faldo_type = faldo:ReverseStrandPosition,
                 -1,
                  0
               )
           ) as ?strand,
         str(?obj_type_name) as ?type,
         str(?label) as ?name,
         str(?obj_name) as ?description,
         ?obj as ?uniqueID,
         ?parent as ?parentUniqueID
  where {
    values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition }
  }"/>
                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="endpoints/test.xml" lines_diff="48"/>
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================

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

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.

**Standalone Instances** enable you to have either a complete JBrowse instance
in a dataset, or just the data directory without JBrowse (e.g. for Apollo).
Currently Galaxy copies the entire JBrowse directory in order to have a
complete, downloadable file that contains a ready-to-go JBrowse
instance. This is obviously an anti-feature because users don't want a
complete copy of JBrowse (12Mb) that's duplicated for every JBrowse
dataset in their history, and admins don't want useless copies of
JBrowse on disk. Unfortunately we have not come up with the perfect
solution just yet, but we're working on it! In the meantime, users have
been given the option to produce just the ``data/`` directory. For those
unfamiliar with JBrowse, the ``data/`` directory contains processed data
files, but no way to view them. This feature is additionally implemented
for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.

**Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
which allows users to specify a non standard genetic code, and have
JBrowse highlight the correct start and stop codons.

**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:: 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