Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 30:8f02a84ee278 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
| author | fubar |
|---|---|
| date | Wed, 21 Feb 2024 02:57:30 +0000 |
| parents | 4ff1ed2065cc |
| children | cb4b32ca9968 |
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| 29:f728cf0df71d | 30:8f02a84ee278 |
|---|---|
| 91 #for $tg in $track_groups: | 91 #for $tg in $track_groups: |
| 92 #for $track in $tg.data_tracks: | 92 #for $track in $tg.data_tracks: |
| 93 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> | 93 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
| 94 #if $track.data_format.data_format_select != "sparql": | 94 #if $track.data_format.data_format_select != "sparql": |
| 95 <files> | 95 <files> |
| 96 #for $dataset in $track.data_format.annotation: | 96 #set dataset = $track.data_format.annotation |
| 97 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> | 97 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> |
| 98 <metadata> | 98 <metadata> |
| 99 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" | 99 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" |
| 100 size="${dataset.get_size(nice_size=True)}" | 100 size="${dataset.get_size(nice_size=True)}" |
| 101 edam_format="${dataset.datatype.edam_format}" | 101 edam_format="${dataset.datatype.edam_format}" |
| 126 tool_id="${dataset.creating_job.tool_id}" | 126 tool_id="${dataset.creating_job.tool_id}" |
| 127 tool_version="${dataset.creating_job.tool_version}" | 127 tool_version="${dataset.creating_job.tool_version}" |
| 128 /> | 128 /> |
| 129 </metadata> | 129 </metadata> |
| 130 </trackFile> | 130 </trackFile> |
| 131 #end for | |
| 132 </files> | 131 </files> |
| 133 #end if | 132 #end if |
| 134 | 133 |
| 135 <options> | 134 <options> |
| 136 | 135 |
| 137 | 136 |
| 138 #if str($track.data_format.data_format_select) == "pileup": | 137 #if str($track.data_format.data_format_select) == "pileup": |
| 139 <pileup> | 138 <pileup> |
| 140 <bam_indices> | 139 <bam_indices> |
| 141 #for $dataset in $track.data_format.annotation: | |
| 142 <bam_index>${dataset.metadata.bam_index}</bam_index> | 140 <bam_index>${dataset.metadata.bam_index}</bam_index> |
| 143 #end for | |
| 144 </bam_indices> | 141 </bam_indices> |
| 145 </pileup> | 142 </pileup> |
| 146 #else if str($track.data_format.data_format_select) == "cram": | 143 #else if str($track.data_format.data_format_select) == "cram": |
| 147 <cram> | 144 <cram> |
| 148 <cram_indices> | 145 <cram_indices> |
| 149 #for $dataset in $track.data_format.annotation: | |
| 150 <cram_index>${dataset.metadata.cram_index}</cram_index> | 146 <cram_index>${dataset.metadata.cram_index}</cram_index> |
| 151 #end for | |
| 152 </cram_indices> | 147 </cram_indices> |
| 153 </cram> | 148 </cram> |
| 154 #else if str($track.data_format.data_format_select) == "blast": | 149 #else if str($track.data_format.data_format_select) == "blast": |
| 155 <blast> | 150 <blast> |
| 156 #if str($track.data_format.blast_parent) != "": | 151 #if str($track.data_format.blast_parent) != "": |
| 232 <conditional name="data_format" label="Track Data Selection Options"> | 227 <conditional name="data_format" label="Track Data Selection Options"> |
| 233 <param type="select" label="Track Type" name="data_format_select"> | 228 <param type="select" label="Track Type" name="data_format_select"> |
| 234 <option value="pileup">BAM Pileup track</option> | 229 <option value="pileup">BAM Pileup track</option> |
| 235 <option value="wiggle">BigWig track</option> | 230 <option value="wiggle">BigWig track</option> |
| 236 <option value="blast">Blast XML track - converted to GFF</option> | 231 <option value="blast">Blast XML track - converted to GFF</option> |
| 237 <option value="cool">cool/mcool/scool data in hdf5 data</option> | 232 <option value="cool">HiC as cool/mcool/scool format files</option> |
| 238 <option value="cram">CRAM</option> | 233 <option value="cram">CRAM</option> |
| 239 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> | 234 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> |
| 240 <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> | 235 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> |
| 241 <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option> | 236 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> |
| 242 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> | 237 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> |
| 243 <option value="sparql">SPARQL</option> | 238 <option value="sparql">SPARQL</option> |
| 244 <option value="vcf">VCF SNP annotation</option> | 239 <option value="vcf">VCF SNP annotation</option> |
| 245 </param> | 240 </param> |
| 246 <when value="blast"> | 241 <when value="blast"> |