Mercurial > repos > fubar > jbrowse2
comparison jbrowse2.xml @ 54:d6b0feb22584 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
| author | fubar |
|---|---|
| date | Thu, 14 Mar 2024 00:59:36 +0000 |
| parents | bdfa6a7c4543 |
| children | 94264fe60478 |
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| 53:bdfa6a7c4543 | 54:d6b0feb22584 |
|---|---|
| 1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_6" profile="22.05"> | 1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05"> |
| 2 <description>genome browser</description> | 2 <description>genome browser</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="edamInc"/> | 6 <expand macro="edamInc"/> |
| 79 </genome> | 79 </genome> |
| 80 #else if str($reference_genome.genome_type_select) == "indexed": | 80 #else if str($reference_genome.genome_type_select) == "indexed": |
| 81 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no"> | 81 <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no"> |
| 82 <metadata> | 82 <metadata> |
| 83 <dataset | 83 <dataset |
| 84 dname = "${reference_genome.genome.refname}" /> | 84 dname = "${reference_genome.genome.fields.name}" /> |
| 85 </metadata> | 85 </metadata> |
| 86 </genome> | 86 </genome> |
| 87 #else | 87 #else |
| 88 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no"> | 88 <genome path="$reference_genome.genome" label="${reference_genome.genome.name}" useuri="no"> |
| 89 <metadata> | 89 <metadata> |
| 318 <param type="select" label="Track Type" name="data_format_select"> | 318 <param type="select" label="Track Type" name="data_format_select"> |
| 319 <option value="bam">BAM Pileup track</option> | 319 <option value="bam">BAM Pileup track</option> |
| 320 <option value="bed">BED track</option> | 320 <option value="bed">BED track</option> |
| 321 <option value="bigwig">BigWig track</option> | 321 <option value="bigwig">BigWig track</option> |
| 322 <option value="blastxml">Blast XML track - converted to GFF</option> | 322 <option value="blastxml">Blast XML track - converted to GFF</option> |
| 323 <option value="cool">HiC as cool/mcool/scool format files</option> | |
| 323 <option value="cram">CRAM</option> | 324 <option value="cram">CRAM</option> |
| 324 <option value="cool">HiC as cool/mcool/scool format files</option> | |
| 325 <option value="gff">GFF/GFF3 feature track</option> | 325 <option value="gff">GFF/GFF3 feature track</option> |
| 326 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> | 326 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> |
| 327 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> | 327 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> |
| 328 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> | 328 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> |
| 329 <option value="vcf">VCF SNP</option> | 329 <option value="vcf">VCF SNP</option> |