comparison jbrowse2.xml @ 21:8e34214ccee4 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aa26b35c213b2ea7c6bb1ab800afc7e03a82508d

20:9c7aa5885721

                        <option value="blast">Blast XML track - converted to GFF</option>
                        <option value="cram">CRAM</option>
                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
                        <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
                        <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option>
                        <option value="sparql">SPARQL</option>
                        <option value="synteny">Synteny track with PAF data</option>
                       <option value="vcf">VCF SNP annotation</option>
                    </param>
                    <when value="blast">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                    </when>
                    <when value="wiggle">
                        <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="synteny">
                        <param label="Comparison genome sequence" help="Paf must use this as the reference to map the real reference sequence"
                            format="fasta"
                            name="synteny_genome"
                            type="data" />
                        <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/>

21:8e34214ccee4

                        <option value="blast">Blast XML track - converted to GFF</option>
                        <option value="cram">CRAM</option>
                        <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
                        <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
                        <option value="maf">Multiple alignment format track. 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="sparql">SPARQL</option>
                       <option value="vcf">VCF SNP annotation</option>
                    </param>
                    <when value="blast">
                        <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />

                    </when>
                    <when value="wiggle">
                        <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 must use this as the reference to map the real reference sequence"
                            format="fasta"
                            name="synteny_genome"
                            type="data" />
                        <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/>