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comparison jbrowse2.xml @ 99:990291e918c7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
author fubar
date Fri, 21 Jun 2024 23:34:31 +0000
parents b1260bca5fdc
children e4ba5f1da6ef
comparison
equal deleted inserted replaced
98:b1260bca5fdc 99:990291e918c7
6 <expand macro="edamInc"/> 6 <expand macro="edamInc"/>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">jbrowse2</xref> 8 <xref type="bio.tools">jbrowse2</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="requirements"/> 10 <expand macro="requirements"/>
11 <expand macro="creators"/>
11 <required_files> 12 <required_files>
12 <include path="autogenJB2.py"/> 13 <include path="autogenJB2.py"/>
13 <include path="blastxml_to_gapped_gff3.py"/> 14 <include path="blastxml_to_gapped_gff3.py"/>
14 <include path="convertMAF.sh"/> 15 <include path="convertMAF.sh"/>
15 <include path="gff3_rebase.py"/> 16 <include path="gff3_rebase.py"/>
26 python '$__tool_directory__/autogenJB2.py' 27 python '$__tool_directory__/autogenJB2.py'
27 #for $key in $autoCollection.keys(): 28 #for $key in $autoCollection.keys():
28 #if $autoCollection[$key].is_collection: 29 #if $autoCollection[$key].is_collection:
29 #set subCol=$autoCollection[$key] 30 #set subCol=$autoCollection[$key]
30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf'] 31 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf']
32 #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in ['fasta.gz','fasta']]
31 #if len($pafs) > 0: 33 #if len($pafs) > 0:
32 --pafmeta '$pafs[0]' 34 --pafmeta '$pafs[0]'
33 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta']
34 #for $ref in $refs: 35 #for $ref in $refs:
35 --pafreferencemeta '$ref' 36 --pafreferencemeta '$ref'
36 #end for 37 #end for
37 #end if 38 #end if
38 #else if $autoCollection[$key].ext == 'fasta': 39 #else if $autoCollection[$key].ext == 'fasta':
312 #end if 313 #end if
313 </root> 314 </root>
314 ]]></configfile> 315 ]]></configfile>
315 </configfiles> 316 </configfiles>
316 <inputs> 317 <inputs>
317 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files"> 318 <repeat name="assemblies" min="1" title="Genome for a set of tracks" help="Tracks will display on this genome coordinates so must all match. Multiple genomes with their own sets of tracks can be added">
318 <conditional name="reference_genome"> 319 <conditional name="reference_genome">
319 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track"> 320 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track">
320 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option> 321 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option>
321 <option value="history">Use a genome fasta file from the current history</option> 322 <option value="history">Use a genome fasta file from the current history</option>
322 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as 323 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as
332 </when> 333 </when>
333 <when value="history"> 334 <when value="history">
334 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/> 335 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/>
335 </when> 336 </when>
336 <when value="uri"> 337 <when value="uri">
337 <param name="uri" type="text" label="URI pointing to tabix compressed fasta"/> 338 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line"
338 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/> 339 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage">
340 </param>
341 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4">
342 </param>
339 </when> 343 </when>
340 </conditional> 344 </conditional>
341 <repeat name="track_groups" title="Track Group"> 345 <repeat name="track_groups" title="Track Group">
342 <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/> 346 <param name="category" type="text" value="Default" optional="False" label="Track Category" 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."/>
343 <repeat name="data_tracks" title="Annotation Track"> 347 <repeat name="data_tracks" title="Annotation Track">
344 <conditional name="data_format" label="Track Data Selection Options"> 348 <conditional name="data_format" label="Track Data Selection Options">
345 <param name="data_format_select" type="select" label="Track Type"> 349 <param name="data_format_select" type="select" label="Track Type">
346 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> 350 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
347 <option value="bed">BED track</option> 351 <option value="bed">BED track</option>
348 <option value="bigwig">BigWig track</option> 352 <option value="bigwig">BigWig track</option>
349 <option value="blastxml">Blast XML track (as GFF3)</option> 353 <option value="blastxml">Blast XML track (as GFF3)</option>
350 <option value="cram">CRAM track, we recomment to convert to BED like for BAM</option> 354 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option>
351 <option value="gff">GFF/GFF3 track</option> 355 <option value="gff">GFF/GFF3 track</option>
352 <option value="cool">HiC as cool/mcool/scool format files</option> 356 <option value="cool">HiC as cool/mcool/scool format files</option>
353 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> 357 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option>
354 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> 358 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
355 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> 359 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option>
356 <option value="vcf">VCF SNP track</option> 360 <option value="vcf">VCF SNP track</option>
357 </param> 361 </param>
358 <when value="blastxml"> 362 <when value="blastxml">
359 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/> 363 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/>
360 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" 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."/> 364 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" 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."/>
402 <expand macro="track_visibility"/> 406 <expand macro="track_visibility"/>
403 </when> 407 </when>
404 <when value="bigwig"> 408 <when value="bigwig">
405 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/> 409 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/>
406 <expand macro="track_visibility"/> 410 <expand macro="track_visibility"/>
411 <expand macro="track_styling_bigwig"/>
407 </when> 412 </when>
408 <when value="paf"> 413 <when value="paf">
409 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> 414 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/>
410 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> 415 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/>
411 <expand macro="track_visibility"/> 416 <expand macro="track_visibility"/>
1127 JBrowse2-in-Galaxy 1132 JBrowse2-in-Galaxy
1128 ================== 1133 ==================
1129 1134
1130 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer. 1135 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer.
1131 1136
1132 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
1133 and detailed track styling is not yet implemented. Please contact us if you are missing features.
1134 1137
1135 Use and local viewing 1138 Use and local viewing
1136 ===================== 1139 =====================
1137 1140
1141 All tracks have a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
1142 There are 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been
1143 used to generate the data:
1144
1145 bam
1146 bed
1147 bigwig
1148 blastxml
1149 cram
1150 gff3
1151 hic
1152 maf
1153 paf
1154 vcf
1155
1156 cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation.
1157 Otherwise conversion to bed is recommended to slim them down.
1158 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended.
1138 1159
1139 A JBrowse2 history item can be opened by viewing it (the "eye" icon). 1160 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
1140
1141 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
1142 This can be shared and viewed without Galaxy.
1143
1144 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
1145 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
1146 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
1147
1148 With python3 installed,
1149
1150 *python3 jb2_webserver.py*
1151
1152 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
1153 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
1154 1161
1155 Overview 1162 Overview
1156 -------- 1163 --------
1157 1164
1158 JBrowse is a fast, embeddable genome browser built completely with 1165 JBrowse is a fast, embeddable genome browser built completely with
1172 1179
1173 Track coordinates and contig names *must* match this reference precisely 1180 Track coordinates and contig names *must* match this reference precisely
1174 or they will not display. 1181 or they will not display.
1175 1182
1176 **Track Groups** represent a set of tracks in a single category. 1183 **Track Groups** represent a set of tracks in a single category.
1184
1177 1185
1178 Annotation Tracks 1186 Annotation Tracks
1179 ----------------- 1187 -----------------
1180 1188
1181 MAF 1189 MAF
1230 10 hits or so. 1238 10 hits or so.
1231 1239
1232 **Protein blast search** option merely informs underlying tools that 1240 **Protein blast search** option merely informs underlying tools that
1233 they should adjust feature locations by 3x. 1241 they should adjust feature locations by 3x.
1234 1242
1243 Local viewing
1244 =============
1245
1246 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
1247 This can be shared and viewed without Galaxy.
1248
1249 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
1250 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
1251 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
1252
1253 With python3 installed,
1254
1255 *python3 jb2_webserver.py*
1256
1257 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
1258 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
1235 1259
1236 ]]></help> 1260 ]]></help>
1237 <expand macro="citations"/> 1261 <expand macro="citations"/>
1238 <expand macro="creators"/> 1262 <expand macro="creators"/>
1239 </tool> 1263 </tool>