Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 15:cce8dacb240f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
| author | fubar |
|---|---|
| date | Thu, 25 Jan 2024 07:39:41 +0000 |
| parents | f5ce31c2f47d |
| children | 1fe91657bfd6 |
comparison
equal
deleted
inserted
replaced
| 14:7c2e28e144f3 | 15:cce8dacb240f |
|---|---|
| 31 <metadata> | 31 <metadata> |
| 32 <genomes> | 32 <genomes> |
| 33 #if str($reference_genome.genome_type_select) == "indexed": | 33 #if str($reference_genome.genome_type_select) == "indexed": |
| 34 <genome path="${reference_genome.genomes.fields.path}" label="${reference_genome.genomes.fields.name}"> | 34 <genome path="${reference_genome.genomes.fields.path}" label="${reference_genome.genomes.fields.name}"> |
| 35 <metadata /> | 35 <metadata /> |
| 36 </genome>s | 36 </genome> |
| 37 #else | 37 #else |
| 38 <genome path="$reference_genome.genome" label="${reference_genome.genome.element_identifier}"> | 38 <genome path="$reference_genome.genome" label="${reference_genome.genome.element_identifier}"> |
| 39 <metadata> | 39 <metadata> |
| 40 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" | 40 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" |
| 41 size="${reference_genome.genome.get_size(nice_size=True)}" | 41 size="${reference_genome.genome.get_size(nice_size=True)}" |
| 295 <expand macro="track_visibility" /> | 295 <expand macro="track_visibility" /> |
| 296 | 296 |
| 297 </when> | 297 </when> |
| 298 | 298 |
| 299 <when value="synteny"> | 299 <when value="synteny"> |
| 300 <param label="Other genome sequence" | 300 <param label="Comparison genome sequence" help="Paf must use this as the reference to map the real reference sequence" |
| 301 format="fasta" | 301 format="fasta" |
| 302 name="synteny_genome" | 302 name="synteny_genome" |
| 303 type="data" /> | 303 type="data" /> |
| 304 | 304 |
| 305 <expand macro="input_conditional" label="Synteny data" format="paf" /> | 305 <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with minimap2 mapping real reference onto desired syntenic reference"/> |
| 306 <expand macro="track_visibility" /> | 306 <expand macro="track_visibility" /> |
| 307 </when> | 307 </when> |
| 308 | 308 |
| 309 <when value="hic"> | 309 <when value="hic"> |
| 310 <!-- TODO no hic datatype by default, but input for hicConvertFormat? hic_matrix datatype on .eu --> | 310 <!-- TODO no hic datatype by default, but input for hicConvertFormat? hic_matrix datatype on .eu --> |