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comparison jbrowse2.xml @ 60:81d535970196 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
author fubar
date Mon, 25 Mar 2024 02:10:05 +0000
parents f807e219cec3
children ab0d6782a95f
comparison
equal deleted inserted replaced
59:f807e219cec3 60:81d535970196
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> 11 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 mkdir -p '$output.files_path' && 13 mkdir -p '$output.files_path' &&
14 ## Copy the XML file into the directory, mostly for debugging
15 ## but nice if users want to reproduce locally
16 cp '$trackxml' '$output.files_path/galaxy.xml' && 14 cp '$trackxml' '$output.files_path/galaxy.xml' &&
17
18 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && 15 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
19
20 #if $jbgen.ucol.formcoll=="collect": 16 #if $jbgen.ucol.formcoll=="collect":
21 python '$__tool_directory__/autogenJB2.py' 17 python '$__tool_directory__/autogenJB2.py'
22 #for $key in $autoCollection.keys(): 18 #for $key in $autoCollection.keys():
23 #if $autoCollection[$key].is_collection: 19 #if $autoCollection[$key].is_collection:
24 #set subCol=$autoCollection[$key] 20 #set subCol=$autoCollection[$key]
137 </metadata> 133 </metadata>
138 <tracks> 134 <tracks>
139 #for $tg in $track_groups: 135 #for $tg in $track_groups:
140 #for $track in $tg.data_tracks: 136 #for $track in $tg.data_tracks:
141 #if $track.data_format.useuri.insource == "uri": 137 #if $track.data_format.useuri.insource == "uri":
142 <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> 138 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
143 <files> 139 <files>
144 <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" 140 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}"
145 label="${track.data_format.useuri.insource.annoname}" useuri="yes"> 141 label="${track.data_format.useuri.annoname}" useuri="yes">
146 <metadata> 142 <metadata>
147 <dataset id = "${track.data_format.useuri.insource.annouri}" /> 143 <dataset id = "${track.data_format.useuri.annouri}" />
148 </metadata> 144 </metadata>
149 </trackFile> 145 </trackFile>
150 </files> 146 </files>
151 <options/>
152 </track>
153 #else if $track.data_format.useuri.insource == "history": 147 #else if $track.data_format.useuri.insource == "history":
154 #if $track.data_format.useuri.annotation: 148 #if $track.data_format.useuri.annotation:
155 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> 149 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
156 <files> 150 <files>
157 #for $dataset in $track.data_format.useuri.annotation: 151 #for $dataset in $track.data_format.useuri.annotation:
158 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> 152 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no">
159 <metadata> 153 <metadata>
160
161 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" 154 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
162 size="${dataset.get_size(nice_size=True)}" 155 size="${dataset.get_size(nice_size=True)}"
163 edam_format="${dataset.datatype.edam_format}" 156 edam_format="${dataset.datatype.edam_format}"
164 file_ext="${dataset.ext}" /> 157 file_ext="${dataset.ext}" />
165 <history id="${__app__.security.encode_id($dataset.history_id)}" 158 <history id="${__app__.security.encode_id($dataset.history_id)}"
191 /> 184 />
192 </metadata> 185 </metadata>
193 </trackFile> 186 </trackFile>
194 #end for 187 #end for
195 </files> 188 </files>
196 189 #end if
197 <options> 190 #end if
198 <style> 191 <options>
199 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]: 192 <style>
200 <type>${track.data_format.jbstyle.track_style.display}</type> 193 #if str($track.data_format.data_format_select) in ["gff", "bed", "vcf", "maf", "blastxml"]:
201 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: 194 <type>${track.data_format.jbstyle.track_style.display}</type>
202 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> 195 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]:
203 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> 196 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels>
204 #end if 197 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions>
205 #end if 198 #end if
206 #if str($track.data_format.data_format_select) in ["bam", "cram"]: 199 #end if
207 <type>LinearAlignmentsDisplay</type> 200 #if str($track.data_format.data_format_select) in ["bam", "cram"]:
208 #end if 201 <type>LinearAlignmentsDisplay</type>
209 #if str($track.data_format.data_format_select) in ["paf"]: 202 #end if
210 <type>LinearBasicDisplay</type> 203 #if str($track.data_format.data_format_select) in ["paf"]:
211 #end if 204 <type>LinearBasicDisplay</type>
212 </style> 205 #end if
206 #if str($track.data_format.data_format_select) in ["hic"]:
207 <type>LinearHicDisplay</type>
208 #end if
209 </style>
213 #if str($track.data_format.data_format_select) == "bam": 210 #if str($track.data_format.data_format_select) == "bam":
214 <bam> 211 <bam>
215 #for $dataset in $track.data_format.useuri.annotation: 212 #for $dataset in $track.data_format.useuri.annotation:
216 <bam_index>${dataset.metadata.bam_index}</bam_index> 213 <bam_index>${dataset.metadata.bam_index}</bam_index>
217 #end for 214 #end for
266 <query_refnames>${track.data_format.query_refnames}</query_refnames> 263 <query_refnames>${track.data_format.query_refnames}</query_refnames>
267 </sparql> 264 </sparql>
268 #end if 265 #end if
269 </options> 266 </options>
270 </track> 267 </track>
271 #end if
272 #end if
273 #end for 268 #end for
274 #end for 269 #end for
275 </tracks> 270 </tracks>
276 </root> 271 </root>
277 #end if 272 #end if