comparison jbrowse.xml @ 10:1a6d882d340d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524

9:f422ba2e9aa5

                    <min_gap>${track.data_format.min_gap}</min_gap>
                    <index>${track.data_format.index}</index>
                </blast>
            #else if str($track.data_format.data_format_select) == "gene_calls":
                <gff>
                    <trackType>${track.data_format.track_class}</trackType>
                  #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>

                    <when value="false" />
                </conditional>

                <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />

                <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>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>

        </repeat>

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

10:1a6d882d340d

                    <min_gap>${track.data_format.min_gap}</min_gap>
                    <index>${track.data_format.index}</index>
                </blast>
            #else if str($track.data_format.data_format_select) == "gene_calls":
                <gff>
                    <trackType>${track.data_format.track_config.track_class}</trackType>
                  #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
                    #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
                    <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
                    #end if
                    #if str($track.data_format.track_config.canvas_options.subParts) != "":
                    <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
                    #end if
                    #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
                    <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
                    #end if
                  #end if
                  #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>

                    <when value="false" />
                </conditional>

                <param label="Index this track" name="index" type="boolean" checked="false" 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="text"
                                   value=""
                                   help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
                                   optional="True"/>
                            <param label="Subfeatures type"
                                   name="subParts"
                                   type="text"
                                   value=""
                                   help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
                                   optional="True"/>
                            <param label="Implied UTRs"
                                   name="impliedUTRs"
                                   type="boolean"
                                   checked="false"
                                   truevalue="true"
                                   falsevalue="false"
                                   help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
                       </section>
                   </when>
                   <when value="JBrowse/View/Track/HTMLFeatures" />
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>

        </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" />
        <param name="standalone" value="Data Directory" />

        <repeat name="track_groups">
            <param name="category" value="With canvas 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>
                    <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>
                    <section name="jbcolor_scale">
                        <conditional name="color_score">
                            <param name="color_score_select" value="none"/>
                        </conditional>
                        <conditional name="color">
                            <param name="color_select" value="automatic"/>
                        </conditional>
                    </section>
                </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
=================