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comparison jbrowse2.xml @ 54:d6b0feb22584 draft

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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
comparison
equal deleted inserted replaced
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>