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comparison jbrowse2.xml @ 30:8f02a84ee278 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
author fubar
date Wed, 21 Feb 2024 02:57:30 +0000
parents 4ff1ed2065cc
children cb4b32ca9968
comparison
equal deleted inserted replaced
29:f728cf0df71d 30:8f02a84ee278
91 #for $tg in $track_groups: 91 #for $tg in $track_groups:
92 #for $track in $tg.data_tracks: 92 #for $track in $tg.data_tracks:
93 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 93 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
94 #if $track.data_format.data_format_select != "sparql": 94 #if $track.data_format.data_format_select != "sparql":
95 <files> 95 <files>
96 #for $dataset in $track.data_format.annotation: 96 #set dataset = $track.data_format.annotation
97 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> 97 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
98 <metadata> 98 <metadata>
99 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 99 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
100 size="${dataset.get_size(nice_size=True)}" 100 size="${dataset.get_size(nice_size=True)}"
101 edam_format="${dataset.datatype.edam_format}" 101 edam_format="${dataset.datatype.edam_format}"
126 tool_id="${dataset.creating_job.tool_id}" 126 tool_id="${dataset.creating_job.tool_id}"
127 tool_version="${dataset.creating_job.tool_version}" 127 tool_version="${dataset.creating_job.tool_version}"
128 /> 128 />
129 </metadata> 129 </metadata>
130 </trackFile> 130 </trackFile>
131 #end for
132 </files> 131 </files>
133 #end if 132 #end if
134 133
135 <options> 134 <options>
136 135
137 136
138 #if str($track.data_format.data_format_select) == "pileup": 137 #if str($track.data_format.data_format_select) == "pileup":
139 <pileup> 138 <pileup>
140 <bam_indices> 139 <bam_indices>
141 #for $dataset in $track.data_format.annotation:
142 <bam_index>${dataset.metadata.bam_index}</bam_index> 140 <bam_index>${dataset.metadata.bam_index}</bam_index>
143 #end for
144 </bam_indices> 141 </bam_indices>
145 </pileup> 142 </pileup>
146 #else if str($track.data_format.data_format_select) == "cram": 143 #else if str($track.data_format.data_format_select) == "cram":
147 <cram> 144 <cram>
148 <cram_indices> 145 <cram_indices>
149 #for $dataset in $track.data_format.annotation:
150 <cram_index>${dataset.metadata.cram_index}</cram_index> 146 <cram_index>${dataset.metadata.cram_index}</cram_index>
151 #end for
152 </cram_indices> 147 </cram_indices>
153 </cram> 148 </cram>
154 #else if str($track.data_format.data_format_select) == "blast": 149 #else if str($track.data_format.data_format_select) == "blast":
155 <blast> 150 <blast>
156 #if str($track.data_format.blast_parent) != "": 151 #if str($track.data_format.blast_parent) != "":
232 <conditional name="data_format" label="Track Data Selection Options"> 227 <conditional name="data_format" label="Track Data Selection Options">
233 <param type="select" label="Track Type" name="data_format_select"> 228 <param type="select" label="Track Type" name="data_format_select">
234 <option value="pileup">BAM Pileup track</option> 229 <option value="pileup">BAM Pileup track</option>
235 <option value="wiggle">BigWig track</option> 230 <option value="wiggle">BigWig track</option>
236 <option value="blast">Blast XML track - converted to GFF</option> 231 <option value="blast">Blast XML track - converted to GFF</option>
237 <option value="cool">cool/mcool/scool data in hdf5 data</option> 232 <option value="cool">HiC as cool/mcool/scool format files</option>
238 <option value="cram">CRAM</option> 233 <option value="cram">CRAM</option>
239 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> 234 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
240 <option value="hic">HiC (compressed binary) track. Existing cool format must be converted to binary hic - hic_matrix will NOT work.</option> 235 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
241 <option value="maf">Multiple alignment format track. Reference name must match the MAF name exactly to work correctly</option> 236 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
242 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 237 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
243 <option value="sparql">SPARQL</option> 238 <option value="sparql">SPARQL</option>
244 <option value="vcf">VCF SNP annotation</option> 239 <option value="vcf">VCF SNP annotation</option>
245 </param> 240 </param>
246 <when value="blast"> 241 <when value="blast">