comparison jbrowse2.xml @ 11:f5ce31c2f47d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168

10:c60b17456297

            <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="pileup">BAM Pileup track</option>
                        <option value="wiggle">BigWig track</option>
                        <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="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" />

                        <param label="Features used in Blast Search"
                            help="in GFF3. This is used  so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."

                            type="boolean"
                            name="is_protein"
                            truevalue="true"
                            falsevalue="false" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>
                        <expand macro="track_visibility" />
                    </when>

11:f5ce31c2f47d

            <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="pileup">BAM Pileup track</option>
                        <option value="wiggle">BigWig track</option>
                        <!-- <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="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" />

                        <param label="Features used in Blast Search"
                            help="in GFF3. This is used  so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."

                            type="boolean"
                            name="is_protein"
                            truevalue="true"
                            falsevalue="false" />
                        <expand macro="track_visibility" />
                    </when> -->
                    <when value="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>
                        <expand macro="track_visibility" />
                    </when>