comparison jbrowse.xml @ 31:2bb2e07a7a21 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c

30:ca2def38369c

                      <iconClass>${menu_item.menu_icon}</iconClass>
                    #end if
                  </menu>
                  #end for
                </menus>
            #end if

            #if str($track.data_format.data_format_select) == "wiggle":
                <wiggle>
                    <type>${track.data_format.xyplot}</type>

        Bookmarks=""
        GCContent="${plugins.GCContent}"
        BlastView="${plugins.BlastView}"
        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>

                        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="vcf">
                <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">

                        classname="feature"
                        label="product,name,id"
                        description="note,description"
                        height="10px"/>
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>
            <when value="pileup">
                <expand macro="input_conditional" label="BAM Track Data" format="bam" />

                <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" />

                <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" />

      <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" />

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

      <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" />

                </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|genome" value="merlin.fa"/>
        <param name="gencode" value="11" />

                    <param name="annotation" value="gff3/1.gff"/>
                    <conditional name="match_part">
                        <param name="match_part_select" value="false"/>
                    </conditional>
                    <conditional name="track_config">
                        <section name="canvas_options">
                            <param name="transcriptType" value="transcript"/>
                            <param name="subParts" value="exon"/>
                            <param name="impliedUTRs" value="true"/>
                        </section>

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

        <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" />
            <repeat name="data_tracks">
                <conditional name="data_format">
                    <param name="data_format_select" value="pileup"/>
                    <param name="annotation" value="bam/merlin-sample.bam"/>
                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="bam/test.xml" lines_diff="48"/>
    </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"/>

                </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
=================

31:2bb2e07a7a21

                      <iconClass>${menu_item.menu_icon}</iconClass>
                    #end if
                  </menu>
                  #end for
                </menus>
            #end if
            #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]:
                <custom_config>
                #for $custom_option in $track.data_format.jb_custom_config.option:
                  <${custom_option.opt_key}>
                    <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}>
                  </${custom_option.opt_key}>
                #end for
                </custom_config>
            #end if

            #if str($track.data_format.data_format_select) == "wiggle":
                <wiggle>
                    <type>${track.data_format.xyplot}</type>

        Bookmarks=""
        GCContent="${plugins.GCContent}"
        BlastView="${plugins.BlastView}"
        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>

                        description="Hit_titles"
                        height="600px"/>
                <expand macro="color_selection"
                        token_scaling_lin_select="false"
                        token_scaling_log_select="true" />
                <expand macro="track_custom_config" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>
            <when value="vcf">
                <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
                <expand macro="track_custom_config" />
                <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">

                        classname="feature"
                        label="product,name,id"
                        description="note,description"
                        height="10px"/>
                <expand macro="color_selection" />
                <expand macro="track_custom_config" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>
            <when value="pileup">
                <expand macro="input_conditional" label="BAM Track Data" format="bam" />

                <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_custom_config" />
                <expand macro="track_display" />
            </when>
            <when value="wiggle">
                <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />

                <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_custom_config" />
                <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" />

      <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="16"/>
    </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="16"/>
    </test>
    <test>
      <param name="reference_genome|genome_type_select" value="history"/>
      <param name="reference_genome|genome" 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="170" />
    </test>
    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" 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="44"/>
    </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="annotation" value="gff3/1.gff"/>
                    <conditional name="match_part">
                        <param name="match_part_select" value="false"/>
                    </conditional>
                    <conditional name="track_config">
                        <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/>
                        <section name="canvas_options">
                            <param name="transcriptType" value="transcript"/>
                            <param name="subParts" value="exon"/>
                            <param name="impliedUTRs" value="true"/>
                        </section>

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

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="track_config/test.xml" lines_diff="30"/>
    </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 custom track config" />
            <repeat name="data_tracks">
                <conditional name="data_format">
                    <param name="data_format_select" value="gene_calls"/>
                    <param name="annotation" value="gff3/1.gff"/>
                    <conditional name="match_part">
                        <param name="match_part_select" value="false"/>
                    </conditional>
                    <section name="jb_custom_config">
                        <repeat name="option">
                            <param name="opt_key" value="displayMode"/>
                            <conditional name="opt_value">
                                <param name="val_type" value="text"/>
                                <param name="val" value="collapsed"/>
                            </conditional>
                        </repeat>
                        <repeat name="option">
                            <param name="opt_key" value="histograms.height"/>
                            <conditional name="opt_value">
                                <param name="val_type" value="integer"/>
                                <param name="val" value="150"/>
                            </conditional>
                        </repeat>
                        <repeat name="option">
                            <param name="opt_key" value="maxFeatureScreenDensity"/>
                            <conditional name="opt_value">
                                <param name="val_type" value="float"/>
                                <param name="val" value="0.1"/>
                            </conditional>
                        </repeat>
                        <repeat name="option">
                            <param name="opt_key" value="style.strandArrow"/>
                            <conditional name="opt_value">
                                <param name="val_type" value="boolean"/>
                                <param name="val" value="false"/>
                            </conditional>
                        </repeat>
                    </section>
                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="custom_config/test.xml" lines_diff="30"/>
    </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">
                <conditional name="data_format">
                    <param name="data_format_select" value="pileup"/>
                    <param name="annotation" value="bam/merlin-sample.bam"/>
                </conditional>
            </repeat>
        </repeat>

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="bam/test.xml" lines_diff="42"/>
    </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="4" />
    </test>

    <test>
        <param name="reference_genome|genome_type_select" value="history"/>
        <param name="reference_genome|genome" value="merlin.fa"/>

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

        <param name="uglyTestingHack" value="enabled" />
        <output name="output" file="endpoints/test.xml" lines_diff="16"/>
    </test>
  </tests>
  <help><![CDATA[
JBrowse-in-Galaxy
=================