Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 35:15da358c3108 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 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Wed, 28 Feb 2024 10:08:57 +0000
parents 2893ef33fba9
children 5f39f745682f
comparison
equal deleted inserted replaced
34:2893ef33fba9 35:15da358c3108
91 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> 91 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
92 </metadata> 92 </metadata>
93 <tracks> 93 <tracks>
94 #for $tg in $track_groups: 94 #for $tg in $track_groups:
95 #for $track in $tg.data_tracks: 95 #for $track in $tg.data_tracks:
96 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 96 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
97 #if $track.data_format.data_format_select != "sparql": 97 #if $track.data_format.data_format_select != "sparql":
98 <files> 98 #for $dataset in $track.data_format.annotation:
99 #set dataset = $track.data_format.annotation 99 <files>
100 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}"> 100 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}">
101 <metadata> 101 <metadata>
102 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 102 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
103 size="${dataset.get_size(nice_size=True)}" 103 size="${dataset.get_size(nice_size=True)}"
104 edam_format="${dataset.datatype.edam_format}" 104 edam_format="${dataset.datatype.edam_format}"
105 file_ext="${dataset.ext}" /> 105 file_ext="${dataset.ext}" />
106 <history id="${__app__.security.encode_id($dataset.history_id)}" 106 <history id="${__app__.security.encode_id($dataset.history_id)}"
107 #if $dataset.history.user: 107 #if $dataset.history.user:
108 user_email="${dataset.history.user.email}" 108 user_email="${dataset.history.user.email}"
109 user_id="${dataset.history.user_id}" 109 user_id="${dataset.history.user_id}"
110 display_name="${dataset.history.get_display_name()}"/> 110 display_name="${dataset.history.get_display_name()}"/>
111 #else 111 #else
112 user_email="anonymous" 112 user_email="anonymous"
113 user_id="-1" 113 user_id="-1"
114 display_name="Unnamed History"/> 114 display_name="Unnamed History"/>
115 #end if 115 #end if
116 <metadata 116 <metadata
117 #for (key, value) in $dataset.get_metadata().items(): 117 #for (key, value) in $dataset.get_metadata().items():
118 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: 118 #if "_types" not in $key and $value is not None and len(str($value)) < 5000:
119 #if isinstance($value, list): 119 #if isinstance($value, list):
120 #set value_str = "[%s]" % ','.join([str(val) for val in value]) 120 #set value_str = "[%s]" % ','.join([str(val) for val in value])
121 ${key}="$value_str" 121 ${key}="$value_str"
122 #else 122 #else
123 ${key}="${value}" 123 ${key}="${value}"
124 #end if 124 #end if
125 #end if 125 #end if
126 #end for
127 />
128 <tool
129 tool_id="${dataset.creating_job.tool_id}"
130 tool_version="${dataset.creating_job.tool_version}"
131 />
132 </metadata>
133 </trackFile>
134 </files>
135 #end for
136 #else
137 <track cat="${tg.category}" format="sparql" visibility="off">
138 #end if
139
140 <options>
141
142 #if str($track.data_format.data_format_select) == "bam":
143 <pileup>
144 #for $dataset in $track.data_format.annotation:
145 <bam_index>${dataset.metadata.bam_index}</bam_index>
126 #end for 146 #end for
127 /> 147 </pileup>
128 <tool 148 #else if str($track.data_format.data_format_select) == "cram":
129 tool_id="${dataset.creating_job.tool_id}" 149 <cram>
130 tool_version="${dataset.creating_job.tool_version}" 150 <cram_indices>
131 /> 151 #for $dataset in $track.data_format.annotation:
132 </metadata> 152 <cram_index>${dataset.metadata.cram_index}</cram_index>
133 </trackFile> 153 #end for
134 </files> 154 </cram_indices>
135 #else 155 </cram>
136 <track cat="${tg.category}" format="sparql" visibility="off"> 156 #else if str($track.data_format.data_format_select) == "blastxml":
137 #end if 157 <blast>
138 158 #if str($track.data_format.blast_parent) != "":
139 <options> 159 <parent>${track.data_format.blast_parent}</parent>
140 160 #end if
141 #if str($track.data_format.data_format_select) == "pileup": 161 <protein>${track.data_format.is_protein}</protein>
142 <pileup> 162 <min_gap>${track.data_format.min_gap}</min_gap>
143 <bam_indices> 163 </blast>
144 <bam_index>${dataset.metadata.bam_index}</bam_index> 164 #else if str($track.data_format.data_format_select) == "gene_calls":
145 </bam_indices> 165 <gff>
146 </pileup> 166 #if $track.data_format.match_part.match_part_select == "true":
147 #else if str($track.data_format.data_format_select) == "cram": 167 <match>${track.data_format.match_part.name}</match>
148 <cram> 168 #end if
149 <cram_indices> 169 </gff>
150 <cram_index>${dataset.metadata.cram_index}</cram_index> 170 #else if str($track.data_format.data_format_select) == "paf":
151 </cram_indices> 171 <paf>
152 </cram> 172 <genome>
153 #else if str($track.data_format.data_format_select) == "blast": 173 #for gnome in $track.data_format.synteny_genome:
154 <blast> 174 $gnome,
155 #if str($track.data_format.blast_parent) != "": 175 #end for
156 <parent>${track.data_format.blast_parent}</parent> 176 </genome>
157 #end if 177 <genome_label>
158 <protein>${track.data_format.is_protein}</protein> 178 #for gnome in $track.data_format.synteny_genome:
159 <min_gap>${track.data_format.min_gap}</min_gap> 179 $gnome.name,
160 </blast> 180 #end for
161 #else if str($track.data_format.data_format_select) == "gene_calls": 181 </genome_label>
162 <gff> 182 </paf>
163 #if $track.data_format.match_part.match_part_select == "true": 183 #else if str($track.data_format.data_format_select) == "hic":
164 <match>${track.data_format.match_part.name}</match> 184 <hic>
165 #end if 185 </hic>
166 </gff> 186 #else if str($track.data_format.data_format_select) == "cool":
167 #else if str($track.data_format.data_format_select) == "paf": 187 <cool>
168 <paf> 188 </cool>
169 <genome> 189 #else if str($track.data_format.data_format_select) == "sparql":
170 #for gnome in $track.data_format.synteny_genome: 190 <label>${track.data_format.label}</label>
171 $gnome, 191 <sparql>
172 #end for 192 <url>${track.data_format.url}</url>
173 </genome> 193 <query>${track.data_format.query}</query>
174 <genome_label> 194 <query_refnames>${track.data_format.query_refnames}</query_refnames>
175 #for gnome in $track.data_format.synteny_genome: 195 </sparql>
176 $gnome.name, 196 #end if
177 #end for 197 </options>
178 </genome_label> 198 </track>
179 </paf> 199 #end for
180 #else if str($track.data_format.data_format_select) == "hic":
181 <hic>
182 </hic>
183 #else if str($track.data_format.data_format_select) == "cool":
184 <cool>
185 </cool>
186 #else if str($track.data_format.data_format_select) == "sparql":
187 <label>${track.data_format.label}</label>
188 <sparql>
189 <url>${track.data_format.url}</url>
190 <query>${track.data_format.query}</query>
191 <query_refnames>${track.data_format.query_refnames}</query_refnames>
192 </sparql>
193 #end if
194 </options>
195 </track>
196 #end for
197 #end for 200 #end for
198 </tracks> 201 </tracks>
199 </root> 202 </root>
200 ]]></configfile> 203 ]]></configfile>
201 </configfiles> 204 </configfiles>
236 value="Default" 239 value="Default"
237 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/> 240 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
238 <repeat name="data_tracks" title="Annotation Track"> 241 <repeat name="data_tracks" title="Annotation Track">
239 <conditional name="data_format" label="Track Data Selection Options"> 242 <conditional name="data_format" label="Track Data Selection Options">
240 <param type="select" label="Track Type" name="data_format_select"> 243 <param type="select" label="Track Type" name="data_format_select">
241 <option value="pileup">BAM Pileup track</option> 244 <option value="bam">BAM Pileup track</option>
242 <option value="wiggle">BigWig track</option> 245 <option value="bigwig">BigWig track</option>
243 <option value="blast">Blast XML track - converted to GFF</option> 246 <option value="blastxml">Blast XML track - converted to GFF</option>
244 <option value="cool">HiC as cool/mcool/scool format files</option> 247 <option value="cool">HiC as cool/mcool/scool format files</option>
245 <option value="cram">CRAM</option> 248 <option value="cram">CRAM</option>
246 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option> 249 <option value="gene_calls" selected="true">GFF/GFF3/BED feature track</option>
247 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> 250 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
248 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> 251 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
249 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 252 <option value="paf">PAF - approximate mapping positions between two set of sequences</option>
250 <option value="sparql">SPARQL</option>
251 <option value="vcf">VCF SNP</option> 253 <option value="vcf">VCF SNP</option>
252 </param> 254 </param>
253 <when value="blast"> 255 <when value="blastxml">
254 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> 256 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
255 257
256 <param label="Features used in Blast Search" 258 <param label="Features used in Blast Search"
257 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this." 259 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
258 format="gff3" 260 format="gff3"
295 </when> 297 </when>
296 <when value="false" /> 298 <when value="false" />
297 </conditional> 299 </conditional>
298 <expand macro="track_visibility" /> 300 <expand macro="track_visibility" />
299 </when> 301 </when>
300 <when value="pileup"> 302 <when value="bam">
301 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> 303 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
302 <expand macro="track_visibility" /> 304 <expand macro="track_visibility" />
303 </when> 305 </when>
304 <when value="cram"> 306 <when value="cram">
305 <expand macro="input_conditional" label="CRAM Track Data" format="cram" /> 307 <expand macro="input_conditional" label="CRAM Track Data" format="cram" />
307 </when> 309 </when>
308 <when value="maf"> 310 <when value="maf">
309 <expand macro="input_conditional" label="MAF Track Data" format="maf" /> 311 <expand macro="input_conditional" label="MAF Track Data" format="maf" />
310 <expand macro="track_visibility" /> 312 <expand macro="track_visibility" />
311 </when> 313 </when>
312 <when value="wiggle"> 314 <when value="bigwig">
313 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> 315 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
314 <expand macro="track_visibility" /> 316 <expand macro="track_visibility" />
315 </when> 317 </when>
316 <when value="paf"> 318 <when value="paf">
317 <param label="Comparison genome sequence" help="Paf from these as the references, using the real reference as the reads to map" 319 <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map"
318 format="fasta" 320 format="fasta"
319 name="synteny_genome" 321 name="synteny_genome"
320 type="data" 322 type="data"
321 multiple="True"/> 323 multiple="True"/>
322 <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/> 324 <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/>
327 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" /> 329 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic" />
328 <expand macro="track_visibility" /> 330 <expand macro="track_visibility" />
329 </when> 331 </when>
330 <when value="cool"> 332 <when value="cool">
331 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" /> 333 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool" />
332 <expand macro="track_visibility" />
333 </when>
334 <when value="sparql">
335 <param type="text" label="SPARQL Server URL" name="url" />
336 <param type="text" label="Track Label" name="label" value="SPARQL Genes" />
337 <param type="text" label="SPARQL Query" name="query" area="true">
338 <sanitizer>
339 <mapping initial="galaxy.util.mapped_chars">
340 <add source="&#10;" target=" " />
341 <add source="&gt;" target="__gt__" />
342 <add source="&lt;" target="__lt__" />
343 </mapping>
344 <valid initial="default">
345 <add value="|" />
346 <add value="#" />
347 <add value="{"/>
348 <add value="}"/>
349 <add value="!"/>
350 <add value="?"/>
351 <add value="&amp;"/>
352 <add value="+"/>
353 <add value="="/>
354 <add value="'"/>
355 <add value='"'/>
356 </valid>
357 </sanitizer>
358 </param>
359 <param type="text" label="SPARQL reference names query" help="This query should return a line for each reference name in a `refName` column" name="query_refnames" area="true">
360 <sanitizer>
361 <mapping initial="galaxy.util.mapped_chars">
362 <add source="&#10;" target=" " />
363 <add source="&gt;" target="__gt__" />
364 <add source="&lt;" target="__lt__" />
365 </mapping>
366 <valid initial="default">
367 <add value="|" />
368 <add value="#" />
369 <add value="{"/>
370 <add value="}"/>
371 <add value="!"/>
372 <add value="?"/>
373 <add value="&amp;"/>
374 <add value="+"/>
375 <add value="="/>
376 <add value="'"/>
377 <add value='"'/>
378 </valid>
379 </sanitizer>
380 </param>
381 <expand macro="track_visibility" /> 334 <expand macro="track_visibility" />
382 </when> 335 </when>
383 </conditional> 336 </conditional>
384 </repeat> 337 </repeat>
385 </repeat> 338 </repeat>