Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 111:0a532764dcfa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9de1453a009c254ab11b16ae8a56cb5c22b131bf-dirty
author fubar
date Tue, 02 Jul 2024 05:08:17 +0000
parents b1260bca5fdc
children 878c27dfea9d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
1 import argparse
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
2 import logging
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
3 import os
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
4 import sys
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
5
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
6 from jbrowse2 import JbrowseConnector as jbC
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
7
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
8
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
9 logging.basicConfig(level=logging.DEBUG)
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
10 log = logging.getLogger("jbrowse")
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
11
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
12 if __name__ == "__main__":
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
13 parser = argparse.ArgumentParser(description="", epilog="")
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
14 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
15 parser.add_argument(
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
16 "--trackmeta",
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
17 help="Repeatable 'filename,filext,filepath,[bai/crai path for filesystem bam/cram]' for JBrowse2 tracks",
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
18 default=[],
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
19 action="append",
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
20 )
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
21 parser.add_argument(
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
22 "--referencemeta",
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
23 help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks - usually only one needed",
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
24 default=[],
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
25 action="append",
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
26 )
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
27 parser.add_argument(
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
28 "--pafmeta",
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
29 help="Repeatable. Each is a 'pafname, filext, filepath, ... ,' for a JBrowse2 paf track",
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
30 default=[],
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
31 action="append",
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
32 )
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
33 parser.add_argument(
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
34 "--pafreferencemeta",
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
35 help="Repeatable. Each is a 'pafname,refpath,refname' Every pafname must have one or more",
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
36 default=[],
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
37 action="append",
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
38 )
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
39 parser.add_argument(
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
40 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
41 )
39
bc57164eb270 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
fubar
parents: 38
diff changeset
42 parser.add_argument("--outdir", help="Output directory", required=True)
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
43 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
44 args = parser.parse_args()
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
45 sessName = args.sessName
77
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
46 default_session_data = {}
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
47 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
48 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
49 refList = [x.strip().split(",") for x in args.referencemeta if x > ""]
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
50 if len(refList) > 0:
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
51 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]]
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
52 # assume no pafs here
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
53 if len(listgenomes) > 0:
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
54 genome_paths = [x[0] for x in listgenomes]
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
55 genome_names = [x[2] for x in listgenomes]
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
56 guseuri = []
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
57 for x in genome_paths:
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
58 if x.startswith("http://") or x.startswith("https://"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
59 guseuri.append("yes")
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
60 else:
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
61 guseuri.append("no")
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
62 jc = jbC(
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
63 outdir=args.outdir,
39
bc57164eb270 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
fubar
parents: 38
diff changeset
64 jbrowse2path=args.jbrowse2path,
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
65 )
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
66 genomes = (
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
67 [
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
68 {
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
69 "path": x,
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
70 "label": genome_names[i],
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
71 "useuri": guseuri[i],
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
72 "meta": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
73 "name": genome_names[i],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
74 "dataset_dname": genome_names[i],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
75 },
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
76 }
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
77 for i, x in enumerate(genome_paths)
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
78 ],
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
79 )
62
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents: 60
diff changeset
80 assref_name = jc.process_genomes(genomes[0])
77
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
81 if not default_session_data.get(assref_name, None):
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
82 default_session_data[assref_name] = {
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
83 "tracks": [],
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
84 "style": {},
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
85 "style_labels": {},
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
86 "visibility": {
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
87 "default_on": [],
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
88 "default_off": [],
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
89 },
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
90 }
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
91 listtracks = trackList
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
92 # foo.paf must have a foo_paf.fasta or fasta.gz to match
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
93 tnames = [x[2] for x in listtracks]
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
94 texts = [x[1] for x in listtracks]
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
95 for i, track in enumerate(listtracks):
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
96 track_conf = {
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
97 "trackfiles": [],
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
98 "category": "autogenerated",
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
99 "assemblyNames": assref_name,
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
100 }
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
101 tpath, trext, trackname = track[:3]
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
102 track_conf["dataset_id"] = trackname
52
ae12977c0e5e planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
103 useuri = "no"
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
104 if tpath.startswith("http://") or tpath.startswith("https://"):
52
ae12977c0e5e planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
105 useuri = "yes"
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
106 if trext == "paf":
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
107 refname = trackname + "_paf.fasta"
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
108 refdat = [x[2] for x in listtracks if x[2] == refname]
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
109 if not refdat:
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
110 jc.logging.warn(
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
111 "No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
112 % (refname, trackname)
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
113 )
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
114 sys.exit(3)
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
115 else:
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
116 track_conf.update(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
117 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
118 "conf": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
119 "options": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
120 "paf": {
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
121 "genome": refdat,
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
122 "genome_label": trackname,
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
123 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
124 }
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
125 }
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
126 }
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
127 )
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
128 elif trext == "bam":
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
129 ipath = track[3]
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
130 if not os.path.exists(ipath):
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
131 ipath = os.path.realpath(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
132 os.path.join(jc.outdir, trackname + ".bai")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
133 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
134 cmd = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
135 "samtools",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
136 "index",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
137 "-b",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
138 "-o",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
139 ipath,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
140 os.path.realpath(track[0]),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
141 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
142 sys.stdout.write("#### calling %s" % " ".join(cmd))
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
143 jc.subprocess_check_call(cmd)
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
144 track_conf.update(
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
145 {"conf": {"options": {"bam": {"bam_index": " %s ~ %s," % (tpath, ipath)}}}}
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
146 )
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
147 elif trext == "cram":
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
148 ipath = track[3]
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
149 if not os.path.exists(ipath):
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
150 ipath = os.path.realpath(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
151 os.path.join("./", trackname + ".crai")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
152 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
153 cmd = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
154 "samtools",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
155 "index",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
156 "-c",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
157 "-o",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
158 ipath,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
159 os.path.realpath(track[0]),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
160 ]
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
161 jc.subprocess_check_call(cmd)
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
162 track_conf.update(
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents: 92
diff changeset
163 {"conf": {"options": {"cram": {"cram_index": "%s ~ %s," % (tpath, ipath)}}}}
57
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents: 53
diff changeset
164 )
48
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
fubar
parents: 46
diff changeset
165 track_conf["path"] = tpath
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
166 track_conf["format"] = trext
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
167 track_conf["name"] = trackname
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
168 track_conf["label"] = trackname
52
ae12977c0e5e planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents: 48
diff changeset
169 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
170 keys = jc.process_annotations(track_conf)
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
171
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
172 if keys:
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
173 for key in keys:
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
174 if trext in [
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
175 "bigwig",
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
176 "gff",
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
177 "gff3",
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
178 "vcf",
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
179 "maf",
72
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e
fubar
parents: 71
diff changeset
180 "bed",
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e
fubar
parents: 71
diff changeset
181 "hic"
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
182 ]:
77
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
183 default_session_data[assref_name]["visibility"]["default_on"].append(key)
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
184 else:
77
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
185 default_session_data[assref_name]["visibility"]["default_off"].append(
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
186 key
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
187 )
60
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
188 if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
189 ttype = "LinearBasicDisplay"
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
190 if trext == "vcf":
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
191 ttype = "LinearVariantDisplay"
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
192 style_json = {
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
193 "type": ttype,
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
194 "trackShowLabels": False,
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
195 "trackShowDescriptions": False,
60
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a
fubar
parents: 57
diff changeset
196 }
77
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
197 default_session_data[assref_name]["style"][key] = style_json
3dcda36b97b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
fubar
parents: 72
diff changeset
198 default_session_data[assref_name]["tracks"].append(key)
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
199 # general_data = {
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
200 # "analytics": root.find("metadata/general/analytics").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
201 # "primary_color": root.find("metadata/general/primary_color").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
202 # "secondary_color": root.find("metadata/general/secondary_color").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
203 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
204 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
205 # "font_size": root.find("metadata/general/font_size").text,
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
206 # }
66
bc10ad1dfb98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 65
diff changeset
207 jc.add_general_configuration({})
65
c81902830900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e
fubar
parents: 62
diff changeset
208 trackconf = jc.config_json.get("tracks", [])
c81902830900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e
fubar
parents: 62
diff changeset
209 for gnome in jc.genome_names:
c81902830900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e
fubar
parents: 62
diff changeset
210 trackconf += jc.tracksToAdd[gnome]
71
e26a8a6d2d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b
fubar
parents: 69
diff changeset
211 logging.debug(
69
7230a2422507 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2c7d6c19a42c421de987ebfdf927c64062ebd79f-dirty
fubar
parents: 67
diff changeset
212 "++++ adding trackconf=%s for gnome %s" % (trackconf, gnome)
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
213 )
65
c81902830900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e
fubar
parents: 62
diff changeset
214 jc.config_json["tracks"] = trackconf
69
7230a2422507 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2c7d6c19a42c421de987ebfdf927c64062ebd79f-dirty
fubar
parents: 67
diff changeset
215 assconf = jc.config_json.get("assemblies", [])
7230a2422507 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2c7d6c19a42c421de987ebfdf927c64062ebd79f-dirty
fubar
parents: 67
diff changeset
216 assconf += jc.assemblies
7230a2422507 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2c7d6c19a42c421de987ebfdf927c64062ebd79f-dirty
fubar
parents: 67
diff changeset
217 jc.config_json["assemblies"] = assconf
71
e26a8a6d2d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b
fubar
parents: 69
diff changeset
218 logging.debug("+++assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
219 jc.write_config()
67
cefe9dbf1d80 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty
fubar
parents: 66
diff changeset
220 default_session_data.update({"session_name": sessName})
35
15da358c3108 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
fubar
parents: 30
diff changeset
221 track_conf.update(default_session_data)
84
5c295cc220ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2dad2139324940fbff8aa089a72641800211e2d9-dirty
fubar
parents: 77
diff changeset
222 jc.add_default_session(default_session_data)
5c295cc220ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2dad2139324940fbff8aa089a72641800211e2d9-dirty
fubar
parents: 77
diff changeset
223 # jc.add_defsess_to_index(default_session_data)
30
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
224 # jc.text_index() not sure what broke here.
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
fubar
parents:
diff changeset
225 else:
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
226 sys.stderr.write(
98
b1260bca5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents: 97
diff changeset
227 "Collection has no suitable trackfiles for autogenJB2 - nothing to process"
46
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents: 39
diff changeset
228 )