comparison jbrowse.xml @ 27:61ce21e36cb5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46

26:08776ba76cf5

                    <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

                        <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                        <option value="JBrowse/View/Track/CanvasFeatures">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"
                                   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" />
                    <when value="BlastView/View/Track/CanvasFeatures" />
                    <when value="NeatHTMLFeatures/View/Track/NeatFeatures" />
                    <when value="NeatCanvasFeatures/View/Track/NeatFeatures" />
                </conditional>
                <expand macro="track_styling" />
                <expand macro="color_selection" />
                <expand macro="track_menu" />
                <expand macro="track_display" />
            </when>
            <when value="pileup">

27:61ce21e36cb5

                    <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 $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
                    #if str($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
                  #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
                    #if str($track.data_format.track_config.html_options.topLevelFeatures) != "":
                    <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures>
                    #end if
                  #end if
                  #if $track.data_format.match_part.match_part_select:
                    <match>${track.data_format.match_part.name}</match>
                  #end if

                        <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
                        <option value="JBrowse/View/Track/CanvasFeatures">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">
                        <expand macro="canvas_options" />
                    </when>
                    <when value="JBrowse/View/Track/HTMLFeatures">
                        <expand macro="html_options" />
                    </when>
                    <when value="BlastView/View/Track/CanvasFeatures" />
                    <when value="NeatHTMLFeatures/View/Track/NeatFeatures">
                        <expand macro="html_options" />
                    </when>
                    <when value="NeatCanvasFeatures/View/Track/NeatFeatures">
                        <expand macro="canvas_options" />
                    </when>
                </conditional>
                <expand macro="track_styling"
                        classname="feature2"
                        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">