comparison jbrowse2.xml @ 48:460d5b6c5d98 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty

47:3e53204c2419

        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
    </metadata>
    <tracks>
        #for $tg in $track_groups:
            #for $track in $tg.data_tracks:
                #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 $track.data_format.useuri.annotation:
                              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">

                            <parent>${track.data_format.blast_parent}</parent>
                          #end if
                            <protein>${track.data_format.is_protein}</protein>
                            <min_gap>${track.data_format.min_gap}</min_gap>
                        </blast>
                    #else if str($track.data_format.data_format_select) == "gene_calls":
                        <gff>
                          #if $track.data_format.match_part.match_part_select == "true":
                            <match>${track.data_format.match_part.name}</match>
                          #end if
                        </gff>

                        <hic>
                        </hic>
                    #else if str($track.data_format.data_format_select) == "cool":
                        <cool>
                        </cool>
                    #else if str($track.data_format.data_format_select) == "sparql":
                        <label>${track.data_format.label}</label>
                        <sparql>
                            <url>${track.data_format.url}</url>
                            <query>${track.data_format.query}</query>

                        </sparql>
                    #end if
                    </options>
                  </track>
                  #end if
                #else if track.data_format.useuri.annouri:
                   <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>
                #end if
            #end for
        #end for
    </tracks>
</root>

                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="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="gene_calls" selected="true">GFF/GFF3/BED 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="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>
                        <expand macro="track_visibility" />
                    </when>
                    <when value="gene_calls">
                        <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
                        <conditional name="match_part" label="match/match_part data">
                        <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
                            <option selected="True" value="false">Not match/match part data</option>
                            <option value="true">Match/match part data</option>
                        </param>

                        </conditional>
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bam">
                        <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cram">
                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                        <expand macro="track_visibility" />

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                            <param name="annotation" value="bed/test-3.bed"/>
                       </conditional>
                    </conditional>

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Auto Coloured" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                           <param name="annotation" value="gff3/A.gff"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Ignore Scale" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                        <param name="annotation" value="gff3/1.gff"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Scaled Colour" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="insource" value= "history"/>
                            <param name="annotation" value="gff3/C.gff"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="annotation" value="gff3/B.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                       <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                       <conditional name="useuri">
                            <param name="annotation" value="gff3/A.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Realistic" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/interpro.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                         <conditional name="useuri">
                            <param name="annotation" value="gff3/2.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="With menu or index" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gene_calls"/>
                         <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <param name="insource" value= "history"/>

            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="With menu or index"/>
                    <has_text text="gene_calls"/>
                </assert_contents>
            </output>
        </test>
        <!-- TODO add a synteny test -->
        <!-- TODO add a bam and a cram test -->

48:460d5b6c5d98

        <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
    </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 $track.data_format.useuri.annotation:
                              <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">

                            <parent>${track.data_format.blast_parent}</parent>
                          #end if
                            <protein>${track.data_format.is_protein}</protein>
                            <min_gap>${track.data_format.min_gap}</min_gap>
                        </blast>
                    #else if str($track.data_format.data_format_select) == "gff":
                        <gff>
                          #if $track.data_format.match_part.match_part_select == "true":
                            <match>${track.data_format.match_part.name}</match>
                          #end if
                        </gff>

                        <hic>
                        </hic>
                    #else if str($track.data_format.data_format_select) == "cool":
                        <cool>
                        </cool>
                    #else if str($track.data_format.data_format_select) == "bed":
                        <bed>
                        </bed>
                    #else if str($track.data_format.data_format_select) == "sparql":
                        <label>${track.data_format.label}</label>
                        <sparql>
                            <url>${track.data_format.url}</url>
                            <query>${track.data_format.query}</query>

                        </sparql>
                    #end if
                    </options>
                  </track>
                  #end if
                #end if
            #end for
        #end for
    </tracks>
</root>

                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" selected="true">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="vcf">
                        <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip" />
                        <expand macro="track_styling_vcf"/>
                        <expand macro="track_visibility" />
                    </when>
                    <when value="gff">
                        <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3" />
                        <conditional name="match_part" label="match/match_part data">
                        <param help="Match part data selection " label="This is match/match_part data" name="match_part_select" type="select">
                            <option selected="True" value="false">Not match/match part data</option>
                            <option value="true">Match/match part data</option>
                        </param>

                        </conditional>
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bam">
                        <expand macro="input_conditional" label="BAM Track Data" format="bam" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="bed">
                        <expand macro="input_conditional" label="BED Track Data" format="bed" />
                        <expand macro="track_visibility" />
                    </when>
                    <when value="cram">
                        <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
                        <expand macro="track_visibility" />

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Default" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="bed"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                            <param name="annotation" value="bed/test-3.bed"/>
                       </conditional>
                    </conditional>

            <param name="reference_genome|genome" value="merlin.fa"/>
            <repeat name="track_groups">
                <param name="category" value="Auto Coloured" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                           <param name="annotation" value="gff3/A.gff"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Ignore Scale" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                       <conditional name="useuri">
                            <param name="insource" value="history"/>
                        <param name="annotation" value="gff3/1.gff"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Scaled Colour" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                       <conditional name="useuri">
                            <param name="insource" value= "history"/>
                            <param name="annotation" value="gff3/C.gff"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                       <conditional name="useuri">
                            <param name="annotation" value="gff3/B.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                       <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                       <conditional name="useuri">
                            <param name="annotation" value="gff3/A.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="Realistic" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/interpro.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                            <param name="annotation" value="gff3/2.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

            <repeat name="track_groups">
                <param name="category" value="With menu or index" />
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                        <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <conditional name="match_part">

                        </section>
                    </conditional>
                </repeat>
                <repeat name="data_tracks">
                    <conditional name="data_format">
                        <param name="data_format_select" value="gff"/>
                         <conditional name="useuri">
                            <param name="annotation" value="gff3/1.gff"/>
                            <param name="insource" value= "history"/>
                        </conditional>
                        <param name="insource" value= "history"/>

            <param name="uglyTestingHack" value="enabled" />
            <output name="output">
                <assert_contents>
                    <has_text text="With menu or index"/>
                    <has_text text="gff"/>
                </assert_contents>
            </output>
        </test>
        <!-- TODO add a synteny test -->
        <!-- TODO add a bam and a cram test -->