comparison jbrowse2.xml @ 59:f807e219cec3 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9

58:0e592dcaeb7f

    </metadata>
    <tracks>
        #for $tg in $track_groups:
            #for $track in $tg.data_tracks:
                #if $track.data_format.useuri.insource == "uri":
                   <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
                      <files>
                        <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes">
                            <metadata>
                            <dataset id = "${track.data_format.useuri.annouri}" />
                            </metadata>
                         </trackFile>
                     </files>
                    <options/>
                </track>
                #else if $track.data_format.useuri.insource == "history":
                    #if $track.data_format.useuri.annotation:
                    <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
                    <files>
                        #for $dataset in $track.data_format.useuri.annotation:

                                <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
                                <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
                            #end if
                        #end if
                        #if str($track.data_format.data_format_select) in ["bam", "cram"]:
                            <type>"LinearAlignmentsDisplay"</type>
                        #end if
                        </style>
                    #if str($track.data_format.data_format_select) == "bam":
                        <bam>
                            #for $dataset in $track.data_format.useuri.annotation:

                          #end if
                        </gff>
                    #else if str($track.data_format.data_format_select) == "paf":
                        <paf>
                            <genome>
                            #for gnome in $track.data_format.synteny_genome:
                                $gnome,
                            #end for
                            </genome>
                            <genome_label>
                            #for gnome in $track.data_format.synteny_genome:
                                $gnome.name,
                            #end for
                            </genome_label>
                        </paf>
                    #else if str($track.data_format.data_format_select) == "hic":
                        <hic>

                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 Data Selection Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="bam">BAM Pileup track</option>
                        <option value="bed">BED track</option>
                        <option value="bigwig">BigWig track</option>
                        <option value="blastxml">Blast XML track - converted to GFF</option>
                        <option value="cool">HiC as cool/mcool/scool format files</option>
                        <option value="cram">CRAM</option>
                        <option value="gff">GFF/GFF3 feature track</option>
                        <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
                        <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
                        <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
                       <option value="vcf">VCF SNP</option>
                    </param>
                    <when value="blastxml">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                        <param label="Features used in Blast Search"

                    <when value="bigwig">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="paf">
                        <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map"
                            format="fasta"
                            name="synteny_genome"
                            type="data"
                            multiple="True"/>
                        <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/>
                        <expand macro="track_visibility" />
                    </when>

                    <when value="hic">
                        <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />

59:f807e219cec3

    </metadata>
    <tracks>
        #for $tg in $track_groups:
            #for $track in $tg.data_tracks:
                #if $track.data_format.useuri.insource == "uri":
                    <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}">
                        <files>
                             <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf"
                                label="${track.data_format.useuri.insource.annoname}" useuri="yes">
                                <metadata>
                                <dataset id = "${track.data_format.useuri.insource.annouri}" />
                                </metadata>
                             </trackFile>
                        </files>
                        <options/>
                    </track>
                #else if $track.data_format.useuri.insource == "history":
                    #if $track.data_format.useuri.annotation:
                    <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
                    <files>
                        #for $dataset in $track.data_format.useuri.annotation:

                                <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
                                <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
                            #end if
                        #end if
                        #if str($track.data_format.data_format_select) in ["bam", "cram"]:
                            <type>LinearAlignmentsDisplay</type>
                        #end if
                        #if str($track.data_format.data_format_select) in ["paf"]:
                            <type>LinearBasicDisplay</type>
                        #end if
                        </style>
                    #if str($track.data_format.data_format_select) == "bam":
                        <bam>
                            #for $dataset in $track.data_format.useuri.annotation:

                          #end if
                        </gff>
                    #else if str($track.data_format.data_format_select) == "paf":
                        <paf>
                            <genome>
                            #for refgenome in $track.data_format.pafuseuri.refgenomes:
                                $refgenome.annotation,
                            #end for
                            </genome>
                            <genome_label>
                            #for refgenome in $track.data_format.pafuseuri.refgenomes:
                                $refgenome.annoname,
                            #end for
                            </genome_label>
                        </paf>
                    #else if str($track.data_format.data_format_select) == "hic":
                        <hic>

                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 Data Selection Options">
                    <param type="select" label="Track Type" name="data_format_select">
                        <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option>
                        <option value="bed">BED track</option>
                        <option value="bigwig">BigWig track</option>
                        <option value="blastxml">Blast XML track (as GFF3)</option>
                        <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option>
                        <option value="gff">GFF/GFF3 track</option>
                        <option value="cool">HiC as cool/mcool/scool format files</option>
                        <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
                        <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
                        <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
                       <option value="vcf">VCF SNP track</option>
                    </param>
                    <when value="blastxml">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                        <param label="Features used in Blast Search"

                    <when value="bigwig">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="paf">
                        <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf"
                             help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
                        <expand macro="pafref_conditional"  label="Comparison genome sequence(s)"
                            format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
                        <expand macro="track_visibility" />
                    </when>

                    <when value="hic">
                        <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />