Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 114:75f01bd05bd8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2f823945594c6e61a7661c253b671a604b8fb959
| author | bgruening |
|---|---|
| date | Tue, 20 Aug 2024 06:43:01 +0000 |
| parents | 878c27dfea9d |
| children | b55199c56abd |
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| 113:878c27dfea9d | 114:75f01bd05bd8 |
|---|---|
| 333 <option value="history">Use a genome fasta file from the current history</option> | 333 <option value="history">Use a genome fasta file from the current history</option> |
| 334 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as | 334 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as |
| 335 tabix bgzip with predictable index file URI</option> | 335 tabix bgzip with predictable index file URI</option> |
| 336 </param> | 336 </param> |
| 337 <when value="indexed"> | 337 <when value="indexed"> |
| 338 <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"> | 338 <param name="genome" type="select" optional="false" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"> |
| 339 <options from_data_table="all_fasta"> | 339 <options from_data_table="all_fasta"> |
| 340 <filter column="2" type="sort_by"/> | 340 <filter column="2" type="sort_by"/> |
| 341 <validator message="No genomes are available for the selected input dataset" type="no_options"/> | 341 <validator message="No genomes are available for the selected input dataset" type="no_options"/> |
| 342 </options> | 342 </options> |
| 343 </param> | 343 </param> |
| 344 </when> | 344 </when> |
| 345 <when value="history"> | 345 <when value="history"> |
| 346 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/> | 346 <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome"/> |
| 347 </when> | 347 </when> |
| 348 <when value="uri"> | 348 <when value="uri"> |
| 349 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" | 349 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" |
| 350 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage"> | 350 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage"> |
| 351 </param> | 351 </param> |
| 1151 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. | 1151 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. |
| 1152 | 1152 |
| 1153 Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been | 1153 Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been |
| 1154 used to generate the data: | 1154 used to generate the data: |
| 1155 | 1155 |
| 1156 :: | |
| 1157 | |
| 1156 bam | 1158 bam |
| 1157 bed | 1159 bed |
| 1158 bigwig | 1160 bigwig |
| 1159 blastxml | 1161 blastxml |
| 1160 cram | 1162 cram |