comparison jbrowse.xml @ 17:ff11d442feed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257

16:b5c5470d7c09

  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command><![CDATA[

#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:

        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome>${reference_genome.genomes.fields.path}</genome>
            #else
              #for $genome in $reference_genome.genomes:
                  <genome>$genome</genome>
              #end for
            #end if
        </genomes>
        <general>
            <defaultLocation>${jbgen.defaultLocation}</defaultLocation>

            <show_nav>${jbgen.show_nav}</show_nav>
            <show_overview>${jbgen.show_overview}</show_overview>
            <show_menu>${jbgen.show_menu}</show_menu>
            <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
        </general>
    </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}">
            <files>
              #for $dataset in $track.data_format.annotation:
              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
              #end for
            </files>

            <options>
            #if str($track.data_format.data_format_select) == "gene_calls" or  str($track.data_format.data_format_select) == "blast":
                <style>
                    <className>${track.data_format.jbstyle.style_classname}</className>
                    <description>${track.data_format.jbstyle.style_description}</description>
                    <label>${track.data_format.jbstyle.style_label}</label>
                    <height>${track.data_format.jbstyle.style_height}</height>
                </style>
                <scaling>
                  #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
                        <method>ignore</method>
                        <scheme>

                    <autoscale>global</autoscale>
                  #else:
                    <min>${track.data_format.scaling.minimum}</min>
                    <max>${track.data_format.scaling.maximum}</max>
                  #end if

                  ## Wiggle tracks need special color config
                  #if str($track.data_format.jbcolor.color.color_select) != "automatic":
                    <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
                    <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>

##                    <query>${track.data_format.query}</query>
##                </sparql>
            #end if
            </options>
        </track>
        #end for
        #end for
    </tracks>
</root>
]]></configfile>
  </configfiles>
  <inputs>
    <conditional name="reference_genome">
        <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
            <option selected="True" value="indexed">Use a built-in genome</option>

        </when>
    </conditional>

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


    <param label="Genetic Code" name="gencode" type="select">
      <option value="1">1. The Standard Code</option>
      <option value="2">2. The Vertebrate Mitochondrial Code</option>
      <option value="3">3. The Yeast Mitochondrial Code</option>
      <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>

    <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" optional="False"/>
    <repeat name="data_tracks" title="Annotation Track">
        <conditional name="data_format">
            <param type="select" label="Track Type" name="data_format_select">
                <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
                <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="sparql">SPARQL</option>-->
            </param>
            <when value="blast">
                <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
                <expand macro="track_display" />
            </when>
            <when value="gene_calls">
                <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
                <conditional name="match_part">
                    <param label="This is match/match_part data"
                           type="boolean"
                           name="match_part_select"
                           truevalue="true"
                           falsevalue="false" />

                <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>
                    </param>
                    <when value="JBrowse/View/Track/CanvasFeatures">
                        <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
                            <param label="Transcript type"
                                   name="transcriptType"

                       type="boolean"
                       name="var_band"
                       truevalue="true"
                       falsevalue="false" />

                <conditional name="scaling">
                    <param type="select" label="Track Scaling" name="scale_select">
                        <option value="auto_local">Autoscale (local)</option>
                        <option value="auto_global" selected="true">Autoscale (global)</option>
                        <option value="fixed">Specify Min/Max</option>
                    </param>

                            type="integer" value="0" />
                        <param label="Track maximum" name="maximum"
                            type="integer" value="100" />
                    </when>
                </conditional>
                <expand macro="color_selection_minmax" />
                <expand macro="track_display" />
            </when>
            <!--
            <when value="sparql">
                <param type="text" label="SPARQL Server URL" name="url" />
                <param type="text" label="Track Label" name="key" value="SPARQL Genes" />

        </conditional>
    </repeat>
    </repeat>

    <expand macro="general_options" />
    <param type="hidden" name="uglyTestingHack" value="" />
  </inputs>
  <outputs>
      <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
  </outputs>

      <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="4"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genomes" value="merlin.fa"/>
      <param name="gencode" value="11" />

            </conditional>
        </repeat>
      </repeat>

      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gff3/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" />

                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="menus/test.xml" lines_diff="6"/>
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genomes" value="merlin.fa"/>
        <param name="gencode" value="11" />

                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="6"/>
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================

JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
alternative to Trackster.

The JBrowse-in-Galaxy (JiG) tool was written to help build complex
JBrowse installations straight from Galaxy, taking advantage of the
latest Galaxy features such as dataset collections, sections, and colour
pickers. It allows you to build up a JBrowse instance without worrying

17:ff11d442feed

  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <version_command>python jbrowse.py --version</version_command>
  <command><![CDATA[

#if $action.action_select == "create":
    mkdir -p $output.files_path &&
#else:

        <genomes>
            #if str($reference_genome.genome_type_select) == "indexed":
              <genome>${reference_genome.genomes.fields.path}</genome>
            #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>

            <show_nav>${jbgen.show_nav}</show_nav>
            <show_overview>${jbgen.show_overview}</show_overview>
            <show_menu>${jbgen.show_menu}</show_menu>
            <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
        </general>
        <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="${dataset.hid}"
                      size="${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)}"
                      user_email="${dataset.history.user.email}"
                      user_id="${dataset.history.user_id}"
                      display_name="${dataset.history.get_display_name()}"/>
                  <metadata
                    #for (key, value) in $dataset.get_metadata().items():
                    #if "_types" not in $key:
                      ${key}="${value}"
                    #end if
                    #end for
                      />
                  <tool
                      tool_id="${dataset.creating_job.tool_id}"
                      tool_version="${dataset.creating_job.tool_version}"
                      />
                </metadata>
              </trackFile>
              #end for
            </files>

            <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>
                    <label>${track.data_format.jbstyle.style_label}</label>
                    <height>${track.data_format.jbstyle.style_height}</height>
                    <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
                </style>
                <scaling>
                  #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
                        <method>ignore</method>
                        <scheme>

                    <autoscale>global</autoscale>
                  #else:
                    <min>${track.data_format.scaling.minimum}</min>
                    <max>${track.data_format.scaling.maximum}</max>
                  #end if
                  <scale>${track.data_format.scale_select2}</scale>

                  ## Wiggle tracks need special color config
                  #if str($track.data_format.jbcolor.color.color_select) != "automatic":
                    <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
                    <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>

##                    <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">
        <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
            <option selected="True" value="indexed">Use a built-in genome</option>

        </when>
    </conditional>

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

    <param label="Genetic Code" name="gencode" type="select">
      <option value="1">1. The Standard Code</option>
      <option value="2">2. The Vertebrate Mitochondrial Code</option>
      <option value="3">3. The Yeast Mitochondrial Code</option>
      <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>

    <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/GBK Features</option>
                <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" />

                <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
                <expand macro="track_display" />
            </when>
            <when value="gene_calls">
                <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
                <conditional name="match_part" label="match/match_part data">
                    <param label="This is match/match_part data"
                           type="boolean"
                           name="match_part_select"
                           truevalue="true"
                           falsevalue="false" />

                <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"

                       type="boolean"
                       name="var_band"
                       truevalue="true"
                       falsevalue="false" />

                <conditional name="scaling" label="Scaling">
                    <param type="select" label="Track Scaling" name="scale_select">
                        <option value="auto_local">Autoscale (local)</option>
                        <option value="auto_global" selected="true">Autoscale (global)</option>
                        <option value="fixed">Specify Min/Max</option>
                    </param>

                            type="integer" value="0" />
                        <param label="Track maximum" name="maximum"
                            type="integer" value="100" />
                    </when>
                </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" />

        </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>
      <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
  </outputs>

      <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" />

            </conditional>
        </repeat>
      </repeat>

      <param name="uglyTestingHack" value="enabled" />
      <output name="output" file="gff3/test.xml" lines_diff="64" />
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genomes" value="merlin.fa"/>
        <param name="gencode" value="11" />

                </conditional>
            </repeat>
        </repeat>

        <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" />

                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="26"/>
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================

JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
alternative to Trackster.

Overview
--------

JBrowse is a fast, embeddable genome browser built completely with
JavaScript and HTML5.

The JBrowse-in-Galaxy (JiG) tool was written to help build complex
JBrowse installations straight from Galaxy, taking advantage of the
latest Galaxy features such as dataset collections, sections, and colour
pickers. It allows you to build up a JBrowse instance without worrying