Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 23:39b717d934a8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
author fubar
date Sat, 03 Feb 2024 10:17:27 +0000
parents 2ddd41a0c2d5
children 4ff1ed2065cc
comparison
equal deleted inserted replaced
22:2ddd41a0c2d5 23:39b717d934a8
1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_3" profile="22.05"> 1 <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_4" 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"/>
171 <genome_label>${track.data_format.synteny_genome.name}</genome_label> 171 <genome_label>${track.data_format.synteny_genome.name}</genome_label>
172 </synteny> 172 </synteny>
173 #else if str($track.data_format.data_format_select) == "hic": 173 #else if str($track.data_format.data_format_select) == "hic":
174 <hic> 174 <hic>
175 </hic> 175 </hic>
176 #else if str($track.data_format.data_format_select) == "cool":
177 <cool>
178 </cool>
176 #else if str($track.data_format.data_format_select) == "sparql": 179 #else if str($track.data_format.data_format_select) == "sparql":
177 <label>${track.data_format.label}</label> 180 <label>${track.data_format.label}</label>
178 <sparql> 181 <sparql>
179 <url>${track.data_format.url}</url> 182 <url>${track.data_format.url}</url>
180 <query>${track.data_format.query}</query> 183 <query>${track.data_format.query}</query>
229 <conditional name="data_format" label="Track Data Selection Options"> 232 <conditional name="data_format" label="Track Data Selection Options">
230 <param type="select" label="Track Type" name="data_format_select"> 233 <param type="select" label="Track Type" name="data_format_select">
231 <option value="pileup">BAM Pileup track</option> 234 <option value="pileup">BAM Pileup track</option>
232 <option value="wiggle">BigWig track</option> 235 <option value="wiggle">BigWig track</option>
233 <option value="blast">Blast XML track - converted to GFF</option> 236 <option value="blast">Blast XML track - converted to GFF</option>
237 <option value="cool">cool/mcool/scool data in hdf5 data</option>
234 <option value="cram">CRAM</option> 238 <option value="cram">CRAM</option>
235 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> 239 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
236 <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> 240 <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option>
237 <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option> 241 <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option>
238 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 242 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
313 317
314 <when value="hic"> 318 <when value="hic">
315 <expand macro="input_conditional" label="HiC data" format="hic" /> 319 <expand macro="input_conditional" label="HiC data" format="hic" />
316 <expand macro="track_visibility" /> 320 <expand macro="track_visibility" />
317 </when> 321 </when>
318 322 <when value="cool">
323 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
324 <expand macro="track_visibility" />
325 </when>
319 <when value="sparql"> 326 <when value="sparql">
320 <param type="text" label="SPARQL Server URL" name="url" /> 327 <param type="text" label="SPARQL Server URL" name="url" />
321 <param type="text" label="Track Label" name="label" value="SPARQL Genes" /> 328 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
322 <param type="text" label="SPARQL Query" name="query" area="true"> 329 <param type="text" label="SPARQL Query" name="query" area="true">
323 <sanitizer> 330 <sanitizer>