Mercurial > repos > fubar > jbrowse2
changeset 54:d6b0feb22584 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
| author | fubar |
|---|---|
| date | Thu, 14 Mar 2024 00:59:36 +0000 |
| parents | bdfa6a7c4543 |
| children | 469c0f6d87d7 |
| files | __pycache__/jbrowse2.cpython-310.pyc jbrowse2.py jbrowse2.xml readme.rst repeathumfish.txt |
| diffstat | 5 files changed, 119 insertions(+), 5 deletions(-) [+] |
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--- a/jbrowse2.py Thu Mar 07 09:23:06 2024 +0000 +++ b/jbrowse2.py Thu Mar 14 00:59:36 2024 +0000 @@ -1085,7 +1085,8 @@ # trouble from spacey names in command lines avoidance if gname not in self.genome_names: # ignore if already there - eg for duplicates among pafs. - asstrack = self.make_assembly(pgpaths[i], gname) + useuri = pgpaths[i].startswith('http://') or pgpaths[i].startswith('https://') + asstrack = self.make_assembly(pgpaths[i], gname, useuri) self.genome_names.append(gname) if self.config_json.get("assemblies", None): self.config_json["assemblies"].append(asstrack)
--- a/jbrowse2.xml Thu Mar 07 09:23:06 2024 +0000 +++ b/jbrowse2.xml Thu Mar 14 00:59:36 2024 +0000 @@ -1,4 +1,4 @@ - <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_6" profile="22.05"> + <tool id="jbrowse2" name="jbrowse2" version="@TOOL_VERSION@+@WRAPPER_VERSION@_7" profile="22.05"> <description>genome browser</description> <macros> <import>macros.xml</import> @@ -81,7 +81,7 @@ <genome path="${reference_genome.genome.fields.path}" label="${reference_genome.genome.fields.name}" useuri="no"> <metadata> <dataset - dname = "${reference_genome.genome.refname}" /> + dname = "${reference_genome.genome.fields.name}" /> </metadata> </genome> #else @@ -320,8 +320,8 @@ <option value="bed">BED track</option> <option value="bigwig">BigWig track</option> <option value="blastxml">Blast XML track - converted to GFF</option> + <option value="cool">HiC as cool/mcool/scool format files</option> <option value="cram">CRAM</option> - <option value="cool">HiC as cool/mcool/scool format files</option> <option value="gff">GFF/GFF3 feature track</option> <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option>
--- a/readme.rst Thu Mar 07 09:23:06 2024 +0000 +++ b/readme.rst Thu Mar 14 00:59:36 2024 +0000 @@ -1,5 +1,12 @@ JBrowse2 in Galaxy ================== +Added Mar 8: + - URI as data source for tracks + - Autogenerate from a collection now builtin to advanced options - ignores form + - potentially thousands of tracks without filling in any form... + - Cram now working + - Multigenome pafs from mashmap working properly.. + - TODO reuse code for references for paf references to allow URI and builtin genomes Added Mar 3: - optional tracks at last for JB2 @@ -24,7 +31,7 @@ JBrowse2 is a fast, embeddable genome browser built completely with JavaScript and HTML5 -Thus, it makes an ideal fit with Galaxy, especially for use as a +Makes an ideal fit with Galaxy, especially for use as a workflow summary. E.g. annotate a genome, then visualise all of the associated datasets as an interactive HTML page. This tool MUST be whitelisted (or ``sanitize_all_html=False`` in galaxy.ini) to function correctly.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repeathumfish.txt Thu Mar 14 00:59:36 2024 +0000 @@ -0,0 +1,106 @@ + Calypte Anna + + ================================================== + file name: rm_input.fasta + sequences: 159 + total length: 1059687259 bp (1043590636 bp excl N/X-runs) + GC level: 41.49 % + bases masked: 79638300 bp ( 7.63 %) + ================================================== + number of length percentage + elements* occupied of sequence + -------------------------------------------------- + SINEs: 32491 3044030 bp 0.29 % + ALUs 0 0 bp 0.00 % + MIRs 23309 1792450 bp 0.17 % + + LINEs: 168150 56100653 bp 5.38 % + LINE1 446 51456 bp 0.00 % + LINE2 3520 419909 bp 0.04 % + L3/CR1 161974 55206716 bp 5.29 % + + LTR elements: 3415 1802798 bp 0.17 % + ERVL 649 266145 bp 0.03 % + ERVL-MaLRs 15 814 bp 0.00 % + ERV_classI 1341 795364 bp 0.08 % + ERV_classII 1159 705705 bp 0.07 % + + DNA elements: 12073 1651025 bp 0.16 % + hAT-Charlie 338 55376 bp 0.01 % + TcMar-Tigger 787 83392 bp 0.01 % + + Unclassified: 3325 445147 bp 0.04 % + + Total interspersed repeats: 63043653 bp 6.04 % + + + Small RNA: 5543 745245 bp 0.07 % + + Satellites: 109 8273 bp 0.00 % + Simple repeats: 284418 12956749 bp 1.24 % + Low complexity: 61652 3494878 bp 0.33 % + ================================================== + + * most repeats fragmented by insertions or deletions + have been counted as one element + Runs of >=20 X/Ns in query were excluded in % calcs + + + The query species was assumed to be homo sapiens + RepeatMasker version 4.1.5 , default mode + + run with rmblastn version 2.13.0+ + FamDB: CONS-Dfam_3.7 + +Amphioxus +================================================== +file name: rm_input.fasta +sequences: 96 +total length: 458494623 bp (458485423 bp excl N/X-runs) +GC level: 41.61 % +bases masked: 9756877 bp ( 2.13 %) +================================================== + number of length percentage + elements* occupied of sequence +-------------------------------------------------- +SINEs: 10212 946135 bp 0.21 % + ALUs 0 0 bp 0.00 % + MIRs 5121 527992 bp 0.12 % + +LINEs: 4019 622661 bp 0.14 % + LINE1 179 11937 bp 0.00 % + LINE2 662 63166 bp 0.01 % + L3/CR1 2144 286741 bp 0.06 % + +LTR elements: 689 138371 bp 0.03 % + ERVL 20 1005 bp 0.00 % + ERVL-MaLRs 4 322 bp 0.00 % + ERV_classI 584 118702 bp 0.03 % + ERV_classII 28 1778 bp 0.00 % + +DNA elements: 850 57478 bp 0.01 % + hAT-Charlie 46 2708 bp 0.00 % + TcMar-Tigger 73 5236 bp 0.00 % + +Unclassified: 517 41430 bp 0.01 % + +Total interspersed repeats: 1806075 bp 0.39 % + + +Small RNA: 5487 857233 bp 0.19 % + +Satellites: 629 50630 bp 0.01 % +Simple repeats: 115914 6556304 bp 1.43 % +Low complexity: 9124 485904 bp 0.11 % +================================================== + +* most repeats fragmented by insertions or deletions + have been counted as one element + Runs of >=20 X/Ns in query were excluded in % calcs + + +The query species was assumed to be homo sapiens +RepeatMasker version 4.1.5 , default mode + +run with rmblastn version 2.13.0+ +FamDB: CONS-Dfam_3.7