jbrowse2: jbrowse2.py annotate

annotate jbrowse2.py @ 95:a0c848f00363 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5903fd8076687ad01a7cf0a522b954106ac6579a

author	fubar
date	Wed, 24 Apr 2024 03:25:23 +0000
parents	4c517a0041a8
children	74074746ccd8

rev	line source
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1 #!/usr/bin/env python
60 81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	2
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	3 import argparse
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	4 import binascii
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	5 import datetime
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	6 import json
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	7 import logging
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	8 import os
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	9 import re
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	10 import shutil
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	11 import ssl
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	12 import struct
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	13 import subprocess
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	14 import tempfile
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	15 import urllib.request
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	16 import xml.etree.ElementTree as ET
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	17 from collections import defaultdict
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	18
65 c81902830900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e fubar parents: 64 diff changeset	19 logging.basicConfig(level=logging.DEBUG)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	20 log = logging.getLogger("jbrowse")
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	21
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	22 JB2VER = "v2.11.0"
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	23 # version pinned if cloning - but not cloning now
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	24 logCommands = True
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	25 # useful for seeing what's being written but not for production setups
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	26 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	27 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	28 GALAXY_INFRASTRUCTURE_URL = None
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	29 mapped_chars = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	30 ">": "__gt__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	31 "<": "__lt__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	32 "'": "__sq__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	33 '"': "__dq__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	34 "[": "__ob__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	35 "]": "__cb__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	36 "{": "__oc__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	37 "}": "__cc__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	38 "@": "__at__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	39 "#": "__pd__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	40 "": "__cn__",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	41 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	42
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	43
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	44 INDEX_TEMPLATE = """<!doctype html>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	45 <html lang="en" style="height:100%">
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	46 <head>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	47 <meta charset="utf-8"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	48 <link rel="shortcut icon" href="./favicon.ico"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	49 <meta name="viewport" content="width=device-width,initial-scale=1"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	50 <meta name="theme-color" content="#000000"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	51 <meta name="description" content="A fast and flexible genome browser"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	52 <link rel="manifest" href="./manifest.json"/>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	53 <title>JBrowse</title>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	54 </script>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	55 </head>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	56 <body style="overscroll-behavior:none; height:100%; margin: 0;">
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	57 <iframe
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	58 id="jbframe"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	59 title="JBrowse2"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	60 frameborder="0"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	61 width="100%"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	62 height="100%"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	63 src='index_noview.html?config=config.json__SESSION_SPEC__'>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	64 </iframe>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	65 </body>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	66 </html>
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	67 """
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	68
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	69
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	70 class ColorScaling(object):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	71
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	72 COLOR_FUNCTION_TEMPLATE = """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	73 function(feature, variableName, glyphObject, track) {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	74 var score = {score};
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	75 {opacity}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	76 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	77 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	78 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	79
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	80 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	81 function(feature, variableName, glyphObject, track) {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	82 var search_up = function self(sf, attr){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	83 if(sf.get(attr) !== undefined){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	84 return sf.get(attr);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	85 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	86 if(sf.parent() === undefined) {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	87 return;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	88 }}else{{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	89 return self(sf.parent(), attr);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	90 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	91 }};
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	92
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	93 var search_down = function self(sf, attr){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	94 if(sf.get(attr) !== undefined){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	95 return sf.get(attr);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	96 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	97 if(sf.children() === undefined) {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	98 return;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	99 }}else{{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	100 var kids = sf.children();
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	101 for(var child_idx in kids){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	102 var x = self(kids[child_idx], attr);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	103 if(x !== undefined){{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	104 return x;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	105 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	106 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	107 return;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	108 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	109 }};
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	110
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	111 var color = ({user_spec_color} \|\| search_up(feature, 'color') \|\| search_down(feature, 'color') \|\| {auto_gen_color});
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	112 var score = (search_up(feature, 'score') \|\| search_down(feature, 'score'));
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	113 {opacity}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	114 if(score === undefined){{ opacity = 1; }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	115 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	116 var red = parseInt(result[1], 16);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	117 var green = parseInt(result[2], 16);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	118 var blue = parseInt(result[3], 16);
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	119 if(isNaN(opacity) \|\| opacity < 0){{ opacity = 0; }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	120 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	121 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	122 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	123
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	124 OPACITY_MATH = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	125 "linear": """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	126 var opacity = (score - ({min})) / (({max}) - ({min}));
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	127 """,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	128 "logarithmic": """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	129 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	130 """,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	131 "blast": """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	132 var opacity = 0;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	133 if(score == 0.0) {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	134 opacity = 1;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	135 }} else {{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	136 opacity = (20 - Math.log10(score)) / 180;
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	137 }}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	138 """,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	139 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	140
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	141 BREWER_COLOUR_IDX = 0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	142 BREWER_COLOUR_SCHEMES = [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	143 (166, 206, 227),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	144 (31, 120, 180),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	145 (178, 223, 138),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	146 (51, 160, 44),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	147 (251, 154, 153),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	148 (227, 26, 28),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	149 (253, 191, 111),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	150 (255, 127, 0),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	151 (202, 178, 214),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	152 (106, 61, 154),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	153 (255, 255, 153),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	154 (177, 89, 40),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	155 (228, 26, 28),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	156 (55, 126, 184),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	157 (77, 175, 74),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	158 (152, 78, 163),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	159 (255, 127, 0),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	160 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	161
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	162 BREWER_DIVERGING_PALLETES = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	163 "BrBg": ("#543005", "#003c30"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	164 "PiYg": ("#8e0152", "#276419"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	165 "PRGn": ("#40004b", "#00441b"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	166 "PuOr": ("#7f3b08", "#2d004b"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	167 "RdBu": ("#67001f", "#053061"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	168 "RdGy": ("#67001f", "#1a1a1a"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	169 "RdYlBu": ("#a50026", "#313695"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	170 "RdYlGn": ("#a50026", "#006837"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	171 "Spectral": ("#9e0142", "#5e4fa2"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	172 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	173
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	174 def __init__(self):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	175 self.brewer_colour_idx = 0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	176
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	177 def rgb_from_hex(self, hexstr):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	178 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	179 return struct.unpack("BBB", binascii.unhexlify(hexstr))
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	180
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	181 def min_max_gff(self, gff_file):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	182 min_val = None
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	183 max_val = None
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	184 with open(gff_file, "r") as handle:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	185 for line in handle:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	186 try:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	187 value = float(line.split("\t")[5])
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	188 min_val = min(value, (min_val or value))
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	189 max_val = max(value, (max_val or value))
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	190
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	191 if value < min_val:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	192 min_val = value
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	193
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	194 if value > max_val:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	195 max_val = value
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	196 except Exception:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	197 pass
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	198 return min_val, max_val
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	199
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	200 def hex_from_rgb(self, r, g, b):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	201 return "#%02x%02x%02x" % (r, g, b)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	202
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	203 def _get_colours(self):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	204 r, g, b = self.BREWER_COLOUR_SCHEMES[
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	205 self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	206 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	207 self.brewer_colour_idx += 1
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	208 return r, g, b
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	209
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	210 def parse_menus(self, track):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	211 trackConfig = {"menuTemplate": [{}, {}, {}, {}]}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	212
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	213 if "menu" in track["menus"]:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	214 menu_list = [track["menus"]["menu"]]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	215 if isinstance(track["menus"]["menu"], list):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	216 menu_list = track["menus"]["menu"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	217
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	218 for m in menu_list:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	219 tpl = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	220 "action": m["action"],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	221 "label": m.get("label", "{name}"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	222 "iconClass": m.get("iconClass", "dijitIconBookmark"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	223 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	224 if "url" in m:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	225 tpl["url"] = m["url"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	226 if "content" in m:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	227 tpl["content"] = m["content"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	228 if "title" in m:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	229 tpl["title"] = m["title"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	230
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	231 trackConfig["menuTemplate"].append(tpl)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	232
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	233 return trackConfig
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	234
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	235 def parse_colours(self, track, trackFormat, gff3=None):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	236 # Wiggle tracks have a bicolor pallete
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	237 trackConfig = {"style": {}}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	238 if trackFormat == "wiggle":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	239
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	240 trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	241 trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	242
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	243 if trackConfig["style"]["pos_color"] == "__auto__":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	244 trackConfig["style"]["neg_color"] = self.hex_from_rgb(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	245 *self._get_colours()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	246 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	247 trackConfig["style"]["pos_color"] = self.hex_from_rgb(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	248 *self._get_colours()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	249 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	250
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	251 # Wiggle tracks can change colour at a specified place
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	252 bc_pivot = track["wiggle"]["bicolor_pivot"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	253 if bc_pivot not in ("mean", "zero"):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	254 # The values are either one of those two strings
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	255 # or a number
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	256 bc_pivot = float(bc_pivot)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	257 trackConfig["bicolor_pivot"] = bc_pivot
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	258 elif "scaling" in track:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	259 if track["scaling"]["method"] == "ignore":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	260 if track["scaling"]["scheme"]["color"] != "__auto__":
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	261 trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	262 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	263 trackConfig["style"]["color"] = self.hex_from_rgb(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	264 *self._get_colours()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	265 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	266 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	267 # Scored method
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	268 algo = track["scaling"]["algo"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	269 # linear, logarithmic, blast
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	270 scales = track["scaling"]["scales"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	271 # type __auto__, manual (min, max)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	272 scheme = track["scaling"]["scheme"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	273 # scheme -> (type (opacity), color)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	274 # ==================================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	275 # GENE CALLS OR BLAST
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	276 # ==================================
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	277 if trackFormat == "blast":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	278 red, green, blue = self._get_colours()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	279 color_function = self.COLOR_FUNCTION_TEMPLATE.format(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	280 **{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	281 "score": "feature._parent.get('score')",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	282 "opacity": self.OPACITY_MATH["blast"],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	283 "red": red,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	284 "green": green,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	285 "blue": blue,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	286 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	287 )
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	288 trackConfig["style"]["color"] = color_function.replace("\n", "")
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	289 elif trackFormat == "gene_calls":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	290 # Default values, based on GFF3 spec
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	291 min_val = 0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	292 max_val = 1000
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	293 # Get min/max and build a scoring function since JBrowse doesn't
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	294 if scales["type"] == "automatic" or scales["type"] == "__auto__":
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	295 min_val, max_val = self.min_max_gff(gff3)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	296 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	297 min_val = scales.get("min", 0)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	298 max_val = scales.get("max", 1000)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	299
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	300 if scheme["color"] == "__auto__":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	301 user_color = "undefined"
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	302 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	303 elif scheme["color"].startswith("#"):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	304 user_color = "'%s'" % self.hex_from_rgb(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	305 *self.rgb_from_hex(scheme["color"][1:])
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	306 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	307 auto_color = "undefined"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	308 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	309 user_color = "undefined"
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	310 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	311
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	312 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	313 **{
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	314 "opacity": self.OPACITY_MATH[algo].format(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	315 **{"max": max_val, "min": min_val}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	316 ),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	317 "user_spec_color": user_color,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	318 "auto_gen_color": auto_color,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	319 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	320 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	321
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	322 trackConfig["style"]["color"] = color_function.replace("\n", "")
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	323 return trackConfig
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	324
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	325
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	326 def etree_to_dict(t):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	327 if t is None:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	328 return {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	329
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	330 d = {t.tag: {} if t.attrib else None}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	331 children = list(t)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	332 if children:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	333 dd = defaultdict(list)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	334 for dc in map(etree_to_dict, children):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	335 for k, v in dc.items():
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	336 dd[k].append(v)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	337 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	338 if t.attrib:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	339 d[t.tag].update(("@" + k, v) for k, v in t.attrib.items())
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	340 if t.text:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	341 text = t.text.strip()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	342 if children or t.attrib:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	343 if text:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	344 d[t.tag]["#text"] = text
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	345 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	346 d[t.tag] = text
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	347 return d
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	348
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	349
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	350 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	351
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	352
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	353 def metadata_from_node(node):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	354 metadata = {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	355 try:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	356 if len(node.findall("dataset")) != 1:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	357 # exit early
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	358 return metadata
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	359 except Exception:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	360 return {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	361
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	362 for (key, value) in node.findall("dataset")[0].attrib.items():
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	363 metadata["dataset_%s" % key] = value
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	364
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	365 if node.findall("history"):
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	366 for (key, value) in node.findall("history")[0].attrib.items():
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	367 metadata["history_%s" % key] = value
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	368
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	369 if node.findall("metadata"):
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	370 for (key, value) in node.findall("metadata")[0].attrib.items():
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	371 metadata["metadata_%s" % key] = value
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	372 # Additional Mappings applied:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	373 metadata[
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	374 "dataset_edam_format"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	375 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	376 metadata["dataset_edam_format"], metadata["dataset_file_ext"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	377 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	378 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format(
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	379 metadata["history_user_email"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	380 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	381 metadata["hist_name"] = metadata["history_display_name"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	382 metadata[
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	383 "history_display_name"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	384 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	385 galaxy=GALAXY_INFRASTRUCTURE_URL,
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	386 encoded_hist_id=metadata.get("history_id", "not available"),
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	387 hist_name=metadata.get("history_display_name", "not available"),
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	388 )
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	389 if node.findall("tool"):
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	390 for (key, value) in node.findall("tool")[0].attrib.items():
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	391 metadata["tool_%s" % key] = value
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	392 metadata[
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	393 "tool_tool"
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	394 ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}{tool_version}</a>'.format(
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	395 galaxy=GALAXY_INFRASTRUCTURE_URL,
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	396 encoded_id=metadata.get("dataset_id", ""),
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	397 tool_id=metadata.get("tool_tool_id", ""),
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	398 tool_version=metadata.get("tool_tool_version", ""),
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	399 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	400 return metadata
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	401
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	402
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	403 class JbrowseConnector(object):
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	404 def __init__(self, outdir, jbrowse2path):
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	405 self.trackCounter = 0 # to avoid name clashes
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	406 self.assemblies = [] # these require more than a few line diff.
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	407 self.assmeta = {}
79 14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	408 self.ass_first_contigs = (
14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	409 []
14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	410 ) # for default session - these are read as first line of the assembly .fai
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	411 self.giURL = GALAXY_INFRASTRUCTURE_URL
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	412 self.outdir = outdir
38 07849bf248e3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767 fubar parents: 37 diff changeset	413 self.jbrowse2path = jbrowse2path
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	414 os.makedirs(self.outdir, exist_ok=True)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	415 self.genome_names = []
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	416 self.trackIdlist = []
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	417 self.tracksToAdd = {}
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	418 self.config_json = {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	419 self.config_json_file = os.path.join(outdir, "config.json")
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	420 self.clone_jbrowse()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	421
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	422 def get_cwd(self, cwd):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	423 if cwd:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	424 return self.outdir
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	425 else:
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	426 return subprocess.check_output(["pwd"]).decode("utf-8").strip()
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	427 # return None
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	428
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	429 def subprocess_check_call(self, command, output=None, cwd=True):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	430 if output:
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	431 if logCommands:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	432 log.debug(
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	433 "cd %s && %s > %s", self.get_cwd(cwd), " ".join(command), output
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	434 )
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	435 subprocess.check_call(command, cwd=self.get_cwd(cwd), stdout=output)
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	436 else:
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	437 if logCommands:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	438 log.debug("cd %s && %s", self.get_cwd(cwd), " ".join(command))
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	439 subprocess.check_call(command, cwd=self.get_cwd(cwd))
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	440
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	441 def subprocess_popen(self, command, cwd=True):
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	442 if logCommands:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	443 log.debug(command)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	444 p = subprocess.Popen(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	445 command,
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	446 cwd=self.get_cwd(cwd),
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	447 shell=True,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	448 stdin=subprocess.PIPE,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	449 stdout=subprocess.PIPE,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	450 stderr=subprocess.PIPE,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	451 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	452 output, err = p.communicate()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	453 retcode = p.returncode
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	454 if retcode != 0:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	455 log.error(command)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	456 log.error(output)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	457 log.error(err)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	458 raise RuntimeError("Command failed with exit code %s" % (retcode))
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	459
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	460 def subprocess_check_output(self, command):
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	461 if logCommands:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	462 log.debug(" ".join(command))
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	463 return subprocess.check_output(command, cwd=self.outdir)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	464
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	465 def symlink_or_copy(self, src, dest):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	466 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	467 os.environ["GALAXY_JBROWSE_SYMLINKS"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	468 ):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	469 cmd = ["ln", "-s", src, dest]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	470 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	471 cmd = ["cp", src, dest]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	472
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	473 return self.subprocess_check_call(cmd)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	474
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	475 def _prepare_track_style(self, trackDict):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	476
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	477 style_data = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	478 "type": "LinearBasicDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	479 "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	480 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	481
5 efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	482 if trackDict.get("displays", None): # use first if multiple like bed
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	483 style_data["type"] = trackDict["displays"][0]["type"]
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	484 style_data["displayId"] = trackDict["displays"][0]["displayId"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	485 return style_data
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	486
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	487 def getNrow(self, url):
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	488 useuri = url.startswith("https://") or url.startswith("http://")
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	489 if not useuri:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	490 fl = open(url, "r").readlines()
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	491 nrow = len(fl)
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	492 else:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	493 try:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	494 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	495 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	496 with urllib.request.urlopen(url, context=scontext) as f:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	497 fl = f.readlines()
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	498 nrow = len(fl)
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	499 except Exception:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	500 nrow = 0
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	501 logging.debug("### getNrow %s returning %d" % (url, nrow))
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	502 return nrow
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	503
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	504 def process_genomes(self, genomes):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	505 assembly = []
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	506 assmeta = []
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	507 useuri = False
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	508 primaryGenome = None
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	509 for i, genome_node in enumerate(genomes):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	510 this_genome = {}
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	511 if genome_node["useuri"] == "yes":
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	512 useuri = True
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	513 genome_name = genome_node["label"].strip()
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	514 if len(genome_name) == 0:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	515 genome_name = os.path.splitext(os.path.basename(genome_node["path"]))[0]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	516 if len(genome_name.split()) > 1:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	517 genome_name = genome_name.split()[0]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	518 # spaces and cruft break scripts when substituted
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	519 if not primaryGenome:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	520 primaryGenome = genome_name
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	521 if genome_name not in self.genome_names:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	522 self.genome_names.append(genome_name)
31 cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty fubar parents: 30 diff changeset	523 fapath = genome_node["path"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	524 if not useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	525 fapath = os.path.realpath(fapath)
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	526 assem, first_contig = self.make_assembly(fapath, genome_name, useuri)
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	527 assembly.append(assem)
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	528 self.ass_first_contigs.append(first_contig)
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	529 if genome_name == primaryGenome: # first one
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	530 this_genome["genome_name"] = genome_name # first one for all tracks
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	531 this_genome["genome_sequence_adapter"] = assem["sequence"][
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	532 "adapter"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	533 ]
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	534 this_genome["genome_firstcontig"] = first_contig
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	535 assmeta.append(this_genome)
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	536 self.assemblies += assembly
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	537 self.assmeta[primaryGenome] = assmeta
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	538 self.tracksToAdd[primaryGenome] = []
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	539 return primaryGenome
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	540
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	541 def make_assembly(self, fapath, gname, useuri):
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	542 """added code to grab the first contig name and length for broken default session from Anthony and Helena's code
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	543 that poor Bjoern is trying to figure out.
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	544 """
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	545 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	546 faname = fapath
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	547 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	548 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	549 with urllib.request.urlopen(url=faname + ".fai", context=scontext) as f:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	550 fl = f.readline()
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	551 contig = fl.decode("utf8").strip()
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	552 # Merlin 172788 8 60 61
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	553 else:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	554 faname = gname + ".fa.gz"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	555 fadest = os.path.realpath(os.path.join(self.outdir, faname))
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	556 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	557 fapath,
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	558 fadest,
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	559 fadest,
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	560 fadest,
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	561 )
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	562 self.subprocess_popen(cmd)
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	563 contig = open(fadest + ".fai", "r").readline().strip()
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	564 adapter = {
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	565 "type": "BgzipFastaAdapter",
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	566 "fastaLocation": {
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	567 "uri": faname,
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	568 },
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	569 "faiLocation": {
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	570 "uri": faname + ".fai",
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	571 },
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	572 "gziLocation": {
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	573 "uri": faname + ".gzi",
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	574 },
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	575 }
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	576 first_contig = contig.split()[:2]
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	577 first_contig.insert(0, gname)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	578 trackDict = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	579 "name": gname,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	580 "sequence": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	581 "type": "ReferenceSequenceTrack",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	582 "trackId": gname,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	583 "adapter": adapter,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	584 },
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	585 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	586 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	587 "type": "LinearReferenceSequenceDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	588 "displayId": "%s-LinearReferenceSequenceDisplay" % gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	589 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	590 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	591 "type": "LinearGCContentDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	592 "displayId": "%s-LinearGCContentDisplay" % gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	593 },
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	594 ],
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	595 }
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	596 return (trackDict, first_contig)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	597
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	598 def add_default_view(self):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	599 cmd = [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	600 "jbrowse",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	601 "set-default-session",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	602 "-s",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	603 self.config_json_file,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	604 "-t",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	605 ",".join(self.trackIdlist),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	606 "-n",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	607 "JBrowse2 in Galaxy",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	608 "--target",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	609 self.config_json_file,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	610 "-v",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	611 " LinearGenomeView",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	612 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	613 self.subprocess_check_call(cmd)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	614
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	615 def write_config(self):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	616 with open(self.config_json_file, "w") as fp:
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	617 json.dump(self.config_json, fp, indent=2)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	618
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	619 def text_index(self):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	620 # Index tracks
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	621 args = [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	622 "jbrowse",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	623 "text-index",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	624 "--target",
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	625 self.outdir,
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	626 "--assemblies",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	627 self.genome_name,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	628 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	629
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	630 tracks = ",".join(self.trackIdlist)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	631 if tracks:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	632 args += ["--tracks", tracks]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	633
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	634 self.subprocess_check_call(args)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	635
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	636 def add_hic(self, data, trackData):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	637 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	638 HiC adapter.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	639 https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	640 for testing locally, these work:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	641 HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	642 using hg19 reference track as a
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	643 'BgzipFastaAdapter'
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	644 fastaLocation:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	645 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	646 faiLocation:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	647 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	648 gziLocation:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	649 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	650 Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
60 81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	651
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	652 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	653 tId = trackData["label"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	654 wasCool = trackData["wasCool"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	655 # can be served - if public.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	656 # dsId = trackData["metadata"]["dataset_id"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	657 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	658 useuri = trackData["useuri"].lower() == "yes"
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	659 logging.debug("wasCool=%s, data=%s, tId=%s" % (wasCool, data, tId))
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	660 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	661 uri = data
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	662 else:
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	663 uri = tId + ".hic"
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	664 if not wasCool:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	665 dest = os.path.join(self.outdir, uri)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	666 if not os.path.exists(dest):
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	667 cmd = ["cp", data, dest]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	668 self.subprocess_check_call(cmd)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	669 else:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	670 logging.error("not wasCool but %s exists" % dest)
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	671 categ = trackData["category"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	672 trackDict = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	673 "type": "HicTrack",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	674 "trackId": tId,
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	675 "name": trackData["name"],
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	676 "assemblyNames": [trackData["assemblyNames"]],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	677 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	678 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	679 ],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	680 "adapter": {"type": "HicAdapter", "hicLocation": {"uri": uri}},
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	681 }
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	682 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	683 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	684
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	685 def add_maf(self, data, trackData):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	686 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	687 from https://github.com/cmdcolin/maf2bed
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	688 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	689 e.g. hg38.chr1 in the sequence identifiers.
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	690 need the reference id - eg hg18, for maf2bed.pl as the first parameter
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	691 """
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	692 tId = trackData["label"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	693 mafPlugin = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	694 "plugins": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	695 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	696 "name": "MafViewer",
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	697 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	698 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	699 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	700 }
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	701 categ = trackData["category"]
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	702 fname = tId
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	703 dest = "%s/%s" % (self.outdir, fname)
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	704 gname = trackData["assemblyNames"]
61 e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty fubar parents: 60 diff changeset	705
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	706 cmd = [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	707 "bash",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	708 os.path.join(INSTALLED_TO, "convertMAF.sh"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	709 data,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	710 gname,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	711 INSTALLED_TO,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	712 dest,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	713 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	714 self.subprocess_check_call(cmd)
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	715 mafs = open(data, "r").readlines()
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	716 mafss = [x for x in mafs if (x.startswith("s\t") or x.startswith("s "))]
61 e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty fubar parents: 60 diff changeset	717 samp = [x.split()[1] for x in mafss if len(x.split()) > 0]
e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty fubar parents: 60 diff changeset	718 sampu = list(dict.fromkeys(samp))
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	719 samples = [x.split(".")[0] for x in sampu]
61 e7a6f7a7148d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 6dde5ad41d63730085116ab2c9a9d3e500a760e4-dirty fubar parents: 60 diff changeset	720 samples.sort()
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	721 if logCommands:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	722 logging.debug(
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	723 "$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	724 % (" ".join(cmd), mafss, samp, samples)
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	725 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	726 trackDict = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	727 "type": "MafTrack",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	728 "trackId": tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	729 "name": trackData["name"],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	730 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	731 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	732 ],
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	733 "adapter": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	734 "type": "MafTabixAdapter",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	735 "samples": samples,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	736 "bedGzLocation": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	737 "uri": fname + ".sorted.bed.gz",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	738 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	739 "index": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	740 "location": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	741 "uri": fname + ".sorted.bed.gz.tbi",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	742 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	743 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	744 },
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	745 "assemblyNames": [trackData["assemblyNames"]],
5 efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	746 "displays": [
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	747 {
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	748 "type": "LinearBasicDisplay",
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	749 "displayId": "%s-LinearBasicDisplay" % tId,
5 efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	750 },
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	751 {"type": "LinearArcDisplay", "displayId": "%s-LinearArcDisplay" % tId},
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	752 ],
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	753 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	754 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	755 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	756 self.tracksToAdd[gname].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	757 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	758 if self.config_json.get("plugins", None):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	759 self.config_json["plugins"].append(mafPlugin[0])
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	760 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	761 self.config_json.update(mafPlugin)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	762
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	763 def _blastxml_to_gff3(self, xml, min_gap=10):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	764 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	765 cmd = [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	766 "python",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	767 os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	768 "--trim",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	769 "--trim_end",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	770 "--include_seq",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	771 "--min_gap",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	772 str(min_gap),
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	773 xml,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	774 ]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	775 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	776 gff3_unrebased.close()
63 ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976 fubar parents: 62 diff changeset	777 logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd))
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	778 return gff3_unrebased.name
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	779
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	780 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	781 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	782 if "parent" in blastOpts and blastOpts["parent"] != "None":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	783 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	784 cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	785 if blastOpts.get("protein", "false") == "true":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	786 cmd.append("--protein2dna")
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	787 cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	788 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
63 ac00dcfb5d1d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976 fubar parents: 62 diff changeset	789 logging.debug("### gff3rebase cmd = %s" % " ".join(cmd))
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	790 gff3_rebased.close()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	791 # Replace original gff3 file
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	792 shutil.copy(gff3_rebased.name, gff3)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	793 os.unlink(gff3_rebased.name)
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	794 self.add_gff(gff3, trackData, **kwargs)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	795
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	796 def add_bigwig(self, data, trackData):
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	797 tId = trackData["label"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	798 useuri = trackData["useuri"].lower() == "yes"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	799 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	800 url = data
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	801 else:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	802 url = tId
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	803 # slashes in names cause path trouble
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	804 dest = os.path.join(self.outdir, url)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	805 cmd = ["cp", data, dest]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	806 self.subprocess_check_call(cmd)
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	807 bwloc = {"uri": url}
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	808 categ = trackData["category"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	809 trackDict = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	810 "type": "QuantitativeTrack",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	811 "trackId": tId,
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	812 "name": trackData["name"],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	813 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	814 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	815 ],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	816 "assemblyNames": [trackData["assemblyNames"]],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	817 "adapter": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	818 "type": "BigWigAdapter",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	819 "bigWigLocation": bwloc,
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	820 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	821 "displays": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	822 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	823 "type": "LinearWiggleDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	824 "displayId": "%s-LinearWiggleDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	825 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	826 ],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	827 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	828 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	829 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	830 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	831 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	832
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	833 def add_bam(self, data, trackData, bam_indexes=None, **kwargs):
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	834 tId = trackData["label"]
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	835 realFName = trackData["path"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	836 useuri = trackData["useuri"].lower() == "yes"
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	837 categ = trackData["category"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	838 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	839 url = data
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	840 else:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	841 fname = tId
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	842 dest = "%s/%s" % (self.outdir, fname)
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	843 self.subprocess_check_call(["cp", data, dest])
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	844 url = fname
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	845 bindex = fname + ".bai"
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	846 bi = bam_indexes.split(",")
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	847 bam_index = [
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	848 x.split(" ~ ")[1].strip()
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	849 for x in bi
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	850 if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	851 ]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	852 logging.debug(
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	853 "===realFName=%s got %s as bam_indexes %s as bi, %s for bam_index"
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	854 % (realFName, bam_indexes, bi, bam_index)
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	855 )
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	856 if len(bam_index) > 0 and os.path.exists(os.path.realpath(bam_index[0])):
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	857 self.subprocess_check_call(["cp", bam_index[0], bindex])
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	858 else:
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	859 cmd = ["samtools", "index", "-b", "-o", bindex, data]
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	860 self.subprocess_check_call(cmd)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	861 trackDict = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	862 "type": "AlignmentsTrack",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	863 "trackId": tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	864 "name": trackData["name"],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	865 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	866 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	867 ],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	868 "assemblyNames": [trackData["assemblyNames"]],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	869 "adapter": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	870 "type": "BamAdapter",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	871 "bamLocation": {"uri": url},
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	872 "index": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	873 "location": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	874 "uri": bindex,
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	875 }
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	876 },
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	877 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	878 "displays": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	879 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	880 "type": "LinearAlignmentsDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	881 "displayId": "%s-LinearAlignmentsDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	882 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	883 ],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	884 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	885 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	886 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	887 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	888 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	889
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	890 def add_cram(self, data, trackData, cram_indexes=None, **kwargs):
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	891 tId = trackData["label"]
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	892 realFName = trackData["path"]
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	893 categ = trackData["category"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	894 useuri = trackData["useuri"].lower() == "yes"
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	895 gsa = self.assmeta.get(trackData["assemblyNames"], None)
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	896 if gsa:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	897 genseqad = gsa[0]["genome_sequence_adapter"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	898 else:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	899 genseqad = "Not found"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	900 logging.warn("No adapter found for cram %s in gsa=%s" % (tId, gsa))
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	901 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	902 url = data
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	903 else:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	904 fname = tId
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	905 dest = os.path.join(self.outdir, fname)
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	906 url = fname
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	907 self.subprocess_check_call(["cp", data, dest])
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	908 ci = cram_indexes.split(",")
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	909 cram_index = [
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	910 x.split(" ~ ")[1].strip()
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	911 for x in ci
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	912 if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	913 ]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	914 logging.debug(
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	915 "===realFName=%s got %s as cram_indexes %s as ci, %s for cram_index"
3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	916 % (realFName, cram_indexes, ci, cram_index)
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	917 )
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	918 if len(cram_index) > 0 and os.path.exists(cram_index[0]):
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	919 if not os.path.exists(dest + ".crai"):
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	920 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	921 self.subprocess_check_call(
92 3c4db8203fad planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78 fubar parents: 89 diff changeset	922 ["cp", os.path.realpath(cram_index[0]), dest + ".crai"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	923 )
53 bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty fubar parents: 50 diff changeset	924 else:
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	925 cpath = os.path.realpath(dest) + ".crai"
53 bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty fubar parents: 50 diff changeset	926 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
bdfa6a7c4543 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty fubar parents: 50 diff changeset	927 self.subprocess_check_call(cmd)
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	928 trackDict = {
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	929 "type": "AlignmentsTrack",
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	930 "trackId": tId,
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	931 "name": trackData["name"],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	932 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	933 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	934 ],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	935 "assemblyNames": [trackData["assemblyNames"]],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	936 "adapter": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	937 "type": "CramAdapter",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	938 "cramLocation": {"uri": url},
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	939 "craiLocation": {
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	940 "uri": url + ".crai",
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	941 },
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	942 "sequenceAdapter": genseqad,
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	943 },
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	944 "displays": [
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	945 {
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	946 "type": "LinearAlignmentsDisplay",
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	947 "displayId": "%s-LinearAlignmentsDisplay" % tId,
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	948 },
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	949 ],
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	950 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	951 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	952 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	953 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	954 self.trackIdlist.append(tId)
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	955
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	956 def add_vcf(self, data, trackData):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	957 tId = trackData["label"]
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	958 # url = "%s/api/datasets/%s/display" % (
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	959 # self.giURL,
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	960 # trackData["metadata"]["dataset_id"],
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	961 # )
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	962 categ = trackData["category"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	963 useuri = trackData["useuri"].lower() == "yes"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	964 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	965 url = data
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	966 else:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	967 url = tId
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	968 dest = "%s/%s" % (self.outdir, url)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	969 cmd = "bgzip -c %s > %s" % (data, dest)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	970 self.subprocess_popen(cmd)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	971 cmd = ["tabix", "-f", "-p", "vcf", dest]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	972 self.subprocess_check_call(cmd)
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	973 trackDict = {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	974 "type": "VariantTrack",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	975 "trackId": tId,
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	976 "name": trackData["name"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	977 "assemblyNames": [trackData["assemblyNames"]],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	978 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	979 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	980 ],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	981 "adapter": {
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	982 "type": "VcfTabixAdapter",
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	983 "vcfGzLocation": {"uri": url},
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	984 "index": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	985 "location": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	986 "uri": url + ".tbi",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	987 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	988 },
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	989 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	990 "displays": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	991 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	992 "type": "LinearVariantDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	993 "displayId": "%s-LinearVariantDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	994 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	995 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	996 "type": "ChordVariantDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	997 "displayId": "%s-ChordVariantDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	998 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	999 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1000 "type": "LinearPairedArcDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1001 "displayId": "%s-LinearPairedArcDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1002 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1003 ],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1004 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1005 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1006 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1007 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1008 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1009
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1010 def _sort_gff(self, data, dest):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1011 # Only index if not already done
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1012 if not os.path.exists(dest):
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1013 cmd = "jbrowse sort-gff '%s' \| bgzip -c > '%s'" % (
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1014 data,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1015 dest,
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1016 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1017 self.subprocess_popen(cmd)
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1018 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1019
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1020 def _sort_bed(self, data, dest):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1021 # Only index if not already done
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1022 if not os.path.exists(dest):
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1023 cmd = "sort -k1,1 -k2,2n '%s' \| bgzip -c > '%s'" % (data, dest)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1024 self.subprocess_popen(cmd)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1025 cmd = ["tabix", "-f", "-p", "bed", dest]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1026 self.subprocess_check_call(cmd)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1027
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1028 def add_gff(self, data, trackData):
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1029 tId = trackData["label"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1030 useuri = trackData["useuri"].lower() == "yes"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1031 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1032 url = trackData["path"]
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1033 else:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1034 url = tId + ".gz"
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1035 dest = "%s/%s" % (self.outdir, url)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1036 self._sort_gff(data, dest)
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1037 categ = trackData["category"]
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1038 trackDict = {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1039 "type": "FeatureTrack",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1040 "trackId": tId,
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1041 "name": trackData["name"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1042 "assemblyNames": [trackData["assemblyNames"]],
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1043 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1044 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1045 ],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1046 "adapter": {
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1047 "type": "Gff3TabixAdapter",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1048 "gffGzLocation": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1049 "uri": url,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1050 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1051 "index": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1052 "location": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1053 "uri": url + ".tbi",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1054 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1055 },
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1056 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1057 "displays": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1058 {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1059 "type": "LinearBasicDisplay",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1060 "displayId": "%s-LinearBasicDisplay" % tId,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1061 },
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1062 {
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1063 "type": "LinearArcDisplay",
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1064 "displayId": "%s-LinearArcDisplay" % tId,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1065 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1066 ],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1067 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1068 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1069 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1070 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1071 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1072
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1073 def add_bed(self, data, ext, trackData):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1074 tId = trackData["label"]
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1075 categ = trackData["category"]
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1076 useuri = trackData["useuri"].lower() == "yes"
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1077 if useuri:
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1078 url = data
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1079 else:
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1080 url = tId + ".gz"
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1081 dest = "%s/%s" % (self.outdir, url)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1082 self._sort_bed(data, dest)
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1083 trackDict = {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1084 "type": "FeatureTrack",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1085 "trackId": tId,
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1086 "name": trackData["name"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1087 "assemblyNames": [trackData["assemblyNames"]],
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1088 "adapter": {
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1089 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1090 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1091 ],
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1092 "type": "BedTabixAdapter",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1093 "bedGzLocation": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1094 "uri": url,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1095 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1096 "index": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1097 "location": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1098 "uri": url + ".tbi",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1099 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1100 },
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1101 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1102 "displays": [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1103 {
9 a26c41e304c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b fubar parents: 7 diff changeset	1104 "type": "LinearBasicDisplay",
a26c41e304c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b fubar parents: 7 diff changeset	1105 "displayId": "%s-LinearBasicDisplay" % tId,
a26c41e304c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b fubar parents: 7 diff changeset	1106 },
a26c41e304c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b fubar parents: 7 diff changeset	1107 {
5 efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	1108 "type": "LinearPileupDisplay",
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	1109 "displayId": "%s-LinearPileupDisplay" % tId,
efc64d8f4b72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9 fubar parents: 3 diff changeset	1110 },
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1111 {
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1112 "type": "LinearArcDisplay",
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1113 "displayId": "%s-LinearArcDisplay" % tId,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1114 },
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1115 ],
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1116 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1117 style_json = self._prepare_track_style(trackDict)
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1118 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1119 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1120 self.trackIdlist.append(tId)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1121
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1122 def add_paf(self, data, trackData, pafOpts, **kwargs):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1123 tname = trackData["name"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1124 tId = trackData["label"]
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1125 url = tId
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1126 useuri = data.startswith("http://") or data.startswith("https://")
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1127 if not useuri:
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1128 dest = "%s/%s" % (self.outdir, url)
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1129 self.symlink_or_copy(os.path.realpath(data), dest)
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1130 nrow = self.getNrow(dest)
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1131 else:
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1132 url = data
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1133 nrow = self.getNrow(url)
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1134 categ = trackData["category"]
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1135 pg = pafOpts["genome"].split(",")
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1136 pgc = [x.strip() for x in pg if x.strip() > ""]
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1137 gnomes = [x.split(" ~ ") for x in pgc]
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1138 logging.debug("pg=%s, gnomes=%s" % (pg, gnomes))
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1139 passnames = [trackData["assemblyNames"]] # always first
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1140 for i, (gpath, gname) in enumerate(gnomes):
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1141 # may have been forgotten by user for uri
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1142 if len(gname) == 0:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1143 gn = os.path.basename(gpath)
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1144 gname = os.path.splitext(gn)[0]
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1145 # trouble from spacey names in command lines avoidance
31 cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty fubar parents: 30 diff changeset	1146 if len(gname.split()) > 1:
cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty fubar parents: 30 diff changeset	1147 gname = gname.split()[0]
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1148 if gname not in passnames:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1149 passnames.append(gname)
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1150 useuri = pafOpts["useuri"] == "true"
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1151 if gname not in self.genome_names:
f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1152 # ignore if already there - eg for duplicates among pafs.
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1153 asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1154 self.genome_names.append(gname)
68 c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1155 self.tracksToAdd[gname] = []
c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1156 self.assemblies.append(asstrack)
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1157 self.ass_first_contigs.append(first_contig)
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1158 trackDict = {
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1159 "type": "SyntenyTrack",
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1160 "trackId": tId,
31 cb4b32ca9968 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty fubar parents: 30 diff changeset	1161 "assemblyNames": passnames,
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1162 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1163 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1164 ],
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1165 "name": tname,
50 f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1166 "adapter": {
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1167 "type": "PAFAdapter",
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1168 "pafLocation": {"uri": url},
f350467f9433 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4 fubar parents: 49 diff changeset	1169 "assemblyNames": passnames,
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1170 },
64 497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1171 "displays": [
68 c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1172 {
c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1173 "type": "LGVSyntenyDisplay",
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1174 "displayId": "%s-LGVSyntenyDisplay" % tId,
68 c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1175 },
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1176 {
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1177 "type": "DotplotDisplay",
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1178 "displayId": "%s-DotplotDisplay" % tId,
2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1179 },
64 497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1180 {
497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1181 "type": "LinearComparativeDisplay",
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1182 "displayId": "%s-LinearComparativeDisplay" % tId,
64 497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1183 },
497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1184 {
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1185 "type": "LinearBasicDisplay",
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1186 "displayId": "%s-LinearSyntenyDisplay" % tId,
64 497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1187 },
497fd2d27aa2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976-dirty fubar parents: 63 diff changeset	1188 ],
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1189 }
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1190 if nrow > 10000:
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1191 style_json = {
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1192 "type": "LGVSyntenyDisplay",
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1193 "displayId": "%s-LGVSyntenyDisplay" % tId,
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1194 }
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1195 else:
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1196 style_json = {
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1197 "type": "LinearBasicDisplay",
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1198 "displayId": "%s-LinearBasicDisplay" % tId,
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1199 }
59 f807e219cec3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 fubar parents: 57 diff changeset	1200 trackDict["style"] = style_json
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1201 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1202 self.trackIdlist.append(tId)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1203
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1204 def process_annotations(self, track):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1205 category = track["category"].replace("__pd__date__pd__", TODAY)
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1206 for trackIndex, (
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1207 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1208 dataset_ext,
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1209 useuri,
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1210 track_human_label,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1211 extra_metadata,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1212 ) in enumerate(track["trackfiles"]):
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1213 if not dataset_path.strip().startswith("http"):
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1214 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1215 for key, value in mapped_chars.items():
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1216 track_human_label = track_human_label.replace(value, key)
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1217 track_human_label = track_human_label.replace(" ", "_")
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1218 outputTrackConfig = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1219 "category": category,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1220 "style": {},
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1221 }
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1222 outputTrackConfig["assemblyNames"] = track["assemblyNames"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1223 outputTrackConfig["key"] = track_human_label
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1224 outputTrackConfig["useuri"] = useuri
48 460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty fubar parents: 47 diff changeset	1225 outputTrackConfig["path"] = dataset_path
460d5b6c5d98 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty fubar parents: 47 diff changeset	1226 outputTrackConfig["ext"] = dataset_ext
7 b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1227
b04fd993b31e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717 fubar parents: 6 diff changeset	1228 outputTrackConfig["trackset"] = track.get("trackset", {})
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1229 outputTrackConfig["label"] = track["label"]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1230 outputTrackConfig["metadata"] = extra_metadata
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1231 outputTrackConfig["name"] = track_human_label
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1232 if track["label"] in self.trackIdlist:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1233 logging.error(
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1234 "### not adding %s already in %s"
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1235 % (track["label"], self.trackIdlist)
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1236 )
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1237 yield None
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1238 if dataset_ext in ("gff", "gff3"):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1239 self.add_gff(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1240 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1241 outputTrackConfig,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1242 )
34 2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd fubar parents: 32 diff changeset	1243 elif dataset_ext in ("hic", "juicebox_hic"):
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1244 outputTrackConfig["wasCool"] = False
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1245 self.add_hic(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1246 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1247 outputTrackConfig,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1248 )
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1249 elif dataset_ext in ("cool", "mcool", "scool"):
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1250 hic_url = outputTrackConfig["label"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1251 hic_path = os.path.join(self.outdir, hic_url) + ".hic"
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1252 outputTrackConfig["wasCool"] = True
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1253 self.subprocess_check_call(
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1254 [
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1255 "hictk",
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1256 "convert",
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1257 "-f",
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1258 "--output-fmt",
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1259 "hic",
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1260 dataset_path,
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1261 hic_path,
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1262 ]
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1263 )
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1264 logging.debug(
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1265 "### ext=cool: wasCool=%s, hic_path=%s"
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1266 % (outputTrackConfig["wasCool"], hic_path)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1267 )
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1268 self.add_hic(
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1269 hic_path,
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1270 outputTrackConfig,
39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1271 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1272 elif dataset_ext in ("bed",):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1273 self.add_bed(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1274 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1275 dataset_ext,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1276 outputTrackConfig,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1277 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1278 elif dataset_ext in ("maf",):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1279 self.add_maf(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1280 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1281 outputTrackConfig,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1282 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1283 elif dataset_ext == "bigwig":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1284 self.add_bigwig(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1285 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1286 outputTrackConfig,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1287 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1288 elif dataset_ext == "bam":
37 7adde511daa1 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty fubar parents: 35 diff changeset	1289 real_indexes = track["conf"]["options"]["bam"]["bam_index"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1290 logging.debug("**** add bam got %s for indexes" % real_indexes)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1291 self.add_bam(
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1292 dataset_path,
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1293 outputTrackConfig,
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1294 bam_indexes=real_indexes,
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1295 )
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	1296 elif dataset_ext == "cram":
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1297 real_indexes = track["conf"]["options"]["cram"]["cram_index"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1298 logging.debug("**** add cram got %s for indexes" % real_indexes)
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	1299 self.add_cram(
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	1300 dataset_path,
bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	1301 outputTrackConfig,
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1302 cram_indexes=real_indexes,
19 bde6b1d09f7d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty fubar parents: 17 diff changeset	1303 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1304 elif dataset_ext == "blastxml":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1305 self.add_blastxml(
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1306 dataset_path,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1307 outputTrackConfig,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1308 track["conf"]["options"]["blast"],
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1309 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1310 elif dataset_ext == "vcf":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1311 self.add_vcf(dataset_path, outputTrackConfig)
15 cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1312 elif dataset_ext == "paf":
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1313 self.add_paf(
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1314 dataset_path,
4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1315 outputTrackConfig,
27 4ff1ed2065cc planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty fubar parents: 25 diff changeset	1316 track["conf"]["options"]["paf"],
15 cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1317 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1318 else:
29 f728cf0df71d planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty fubar parents: 28 diff changeset	1319 logging.warn("Do not know how to handle %s", dataset_ext)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1320 # Return non-human label for use in other fields
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1321 yield outputTrackConfig["label"]
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1322
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1323 def add_default_session(self, default_data):
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1324 """
60 81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1325 default session settings are hard and fragile.
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1326 .add_default_view() and other configuration code adapted from
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1327 https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1328 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1329 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1330 track_types = {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1331 with open(self.config_json_file, "r") as config_file:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1332 config_json = json.load(config_file)
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1333 if self.config_json:
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1334 config_json.update(self.config_json)
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1335 if "defaultSession" in config_json:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1336 session_json = config_json["defaultSession"]
78 7bb6259ea52f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 76 diff changeset	1337 session_views = []
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1338 else:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1339 session_json = {}
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1340 session_views = []
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1341 for gnome in self.assmeta.keys(): # assemblies have their own tracks
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1342 tracks_data = []
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1343 for track_conf in self.tracksToAdd[gnome]:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1344 tId = track_conf["trackId"]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1345 if tId in default_data[gnome]["visibility"]["default_on"]:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1346 track_types[tId] = track_conf["type"]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1347 style_data = default_data[gnome]["style"].get(tId, None)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1348 if not style_data:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1349 logging.debug(
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1350 "### No style data for %s in available default data %s"
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1351 % (tId, default_data)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1352 )
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1353 style_data = {"type": "LinearBasicDisplay"}
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1354 if "displays" in track_conf:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1355 disp = track_conf["displays"][0]["type"]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1356 style_data["type"] = disp
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1357 if track_conf.get("style_labels", None):
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1358 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1359 # TODO move this to per track displays?
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1360 style_data["labels"] = track_conf["style_labels"]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1361 tracks_data.append(
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1362 {
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1363 "type": track_types[tId],
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1364 "configuration": tId,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1365 "displays": [style_data],
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1366 }
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1367 )
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1368 view_json = {
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1369 "type": "LinearGenomeView",
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1370 "offsetPx": 0,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1371 "minimized": False,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1372 "tracks": tracks_data,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1373 }
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1374 first = [x for x in self.ass_first_contigs if x[0] == gnome]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1375 if len(first) > 0:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1376 [gnome, refName, end] = first[0]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1377 start = 0
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1378 end = int(end)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1379 drdict = {
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1380 "refName": refName,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1381 "start": start,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1382 "end": end,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1383 "reversed": False,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1384 "assemblyName": gnome,
79 14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	1385 }
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1386 else:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1387 ddl = default_data.get("defaultLocation", None)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1388 if ddl:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1389 loc_match = re.search(r"^([^:]+):([\d,])\.([\d,]*)$", ddl)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1390 # allow commas like 100,000 but ignore as integer
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1391 if loc_match:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1392 refName = loc_match.group(1)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1393 drdict["refName"] = refName
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1394 if loc_match.group(2) > "":
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1395 drdict["start"] = int(loc_match.group(2).replace(",", ""))
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1396 if loc_match.group(3) > "":
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1397 drdict["end"] = int(loc_match.group(3).replace(",", ""))
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1398 else:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1399 logging.info(
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1400 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1401 % ddl
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1402 )
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1403 if drdict.get("refName", None):
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1404 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1405 view_json["displayedRegions"] = [
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1406 drdict,
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1407 ]
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1408 logging.info("@@@ defaultlocation %s for default session" % drdict)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1409 else:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1410 logging.info(
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1411 "@@@ no track location for default session - please add one!"
79 14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	1412 )
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1413 session_views.append(view_json)
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1414 session_name = default_data.get("session_name", "New session")
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1415 for key, value in mapped_chars.items():
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1416 session_name = session_name.replace(value, key)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1417 session_json["name"] = session_name
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1418
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1419 if "views" not in session_json:
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1420 session_json["views"] = session_views
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1421 else:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1422 session_json["views"] += session_views
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1423 pp = json.dumps(session_views, indent=2)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1424 config_json["defaultSession"] = session_json
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1425 self.config_json.update(config_json)
72 2bdb748df098 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 9d5e563dde653450723415b0fccd2ebb4b82477e fubar parents: 71 diff changeset	1426 logging.debug("defaultSession=%s" % (pp))
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1427 with open(self.config_json_file, "w") as config_file:
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1428 json.dump(self.config_json, config_file, indent=2)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1429
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1430 def add_defsess_to_index(self, data):
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1431 """
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1432 PROBABLY NOW BROKEN by changes since this was deprecated temporarily as at April 18
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1433
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1434 Included on request of the new codeowner, from Anthony's IUC PR.
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1435 Had to be fixed to keep each assembly with the associated tracks for a default view.
dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1436 Originally used only the first assembly, putting all tracks there and so breaking some
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1437 when tested with 2 or more.
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1438
79 14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	1439 ----------------------------------------------------------
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1440 Add some default session settings: set some assemblies/tracks on/off
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1441
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1442 This allows to select a default view:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1443 - jb type (Linear, Circular, etc)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1444 - default location on an assembly
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1445 - default tracks
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1446 - ...
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1447
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1448 Different methods to do that were tested/discussed:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1449 - using a defaultSession item in config.json: this proved to be difficult:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1450 forced to write a full session block, including hard-coded/hard-to-guess items,
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1451 no good way to let Jbrowse2 display a scaffold without knowing its size
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1452 - using JBrowse2 as an embedded React component in a tool-generated html file:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1453 it works but it requires generating js code to actually do what we want = chosing default view, assembly, tracks, ...
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1454 - writing a session-spec inside the config.json file: this is not yet supported as of 2.10.2 (see PR 4148 below)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1455 a session-spec is a kind of simplified defaultSession where you don't need to specify every aspect of the session
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1456 - passing a session-spec through URL params by embedding the JBrowse2 index.html inside an iframe
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1457 we selected this option
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1458
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1459 Xrefs to understand the choices:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1460 https://github.com/GMOD/jbrowse-components/issues/2708
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1461 https://github.com/GMOD/jbrowse-components/discussions/3568
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1462 https://github.com/GMOD/jbrowse-components/pull/4148
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1463 """
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1464 new_index = "Nothing written"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1465 session_spec = {"views": []}
74 13ede71c3a4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b fubar parents: 73 diff changeset	1466 logging.debug("def ass_first=%s\ndata=%s" % (self.ass_first_contigs, data))
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1467 for first_contig in self.ass_first_contigs:
75 9c8459ce7d88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 74 diff changeset	1468 logging.debug("first contig=%s" % self.ass_first_contigs)
9c8459ce7d88 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 74 diff changeset	1469 [gnome, refName, end] = first_contig
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1470 start = 0
76 9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1471 aview = {
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1472 "assembly": gnome,
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1473 "loc": "{}:{}..{}".format(refName, start, end),
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1474 "type": "LinearGenomeView",
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1475 "tracks": data[gnome]["tracks"],
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1476 }
9e3eb6b26f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 75 diff changeset	1477 session_spec["views"].append(aview)
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1478 sess = json.dumps(session_spec, sort_keys=True, indent=2)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1479 new_index = INDEX_TEMPLATE.replace(
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1480 "__SESSION_SPEC__", "&session=spec-{}".format(sess)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1481 )
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1482
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1483 os.rename(
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1484 os.path.join(self.outdir, "index.html"),
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1485 os.path.join(self.outdir, "index_noview.html"),
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1486 )
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1487
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1488 with open(os.path.join(self.outdir, "index.html"), "w") as nind:
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1489 nind.write(new_index)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1490 logging.debug(
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1491 "#### add_defsession gnome=%s refname=%s\nsession_spec=%s\nnew_index=%s"
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1492 % (gnome, refName, sess, new_index)
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1493 )
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1494
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1495 def add_general_configuration(self, data):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1496 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1497 Add some general configuration to the config.json file
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1498 """
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1499
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1500 config_path = self.config_json_file
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1501 if os.path.exists(config_path):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1502 with open(config_path, "r") as config_file:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1503 config_json = json.load(config_file)
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1504 else:
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1505 config_json = {}
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1506 if self.config_json:
c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1507 config_json.update(self.config_json)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1508 config_data = {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1509
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1510 config_data["disableAnalytics"] = data.get("analytics", "false") == "true"
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1511
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1512 config_data["theme"] = {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1513 "palette": {
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1514 "primary": {"main": data.get("primary_color", "#0D233F")},
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1515 "secondary": {"main": data.get("secondary_color", "#721E63")},
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1516 "tertiary": {"main": data.get("tertiary_color", "#135560")},
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1517 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1518 },
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1519 "typography": {"fontSize": int(data.get("font_size", 10))},
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1520 }
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1521 if not config_json.get("configuration", None):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1522 config_json["configuration"] = {}
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1523 config_json["configuration"].update(config_data)
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1524 self.config_json.update(config_json)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1525 with open(config_path, "w") as config_file:
10 c60b17456297 planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04 fubar parents: 9 diff changeset	1526 json.dump(self.config_json, config_file, indent=2)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1527
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1528 def clone_jbrowse(self, realclone=False):
60 81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1529 """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1530 Leave as True between version updates on temporary tools - requires manual conda trigger :(
81d535970196 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 403a35e1245fa5e62f4be6116a725b9e4d9c353a fubar parents: 59 diff changeset	1531 """
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1532 dest = self.outdir
56 c0097a584a8a planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674 fubar parents: 55 diff changeset	1533 if realclone:
57 94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1534 self.subprocess_check_call(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1535 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty fubar parents: 56 diff changeset	1536 )
56 c0097a584a8a planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674 fubar parents: 55 diff changeset	1537 else:
c0097a584a8a planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674 fubar parents: 55 diff changeset	1538 shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1539 for fn in [
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1540 "asset-manifest.json",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1541 "favicon.ico",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1542 "robots.txt",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1543 "umd_plugin.js",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1544 "version.txt",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1545 "test_data",
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1546 ]:
38 07849bf248e3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767 fubar parents: 37 diff changeset	1547 cmd = ["rm", "-rf", os.path.join(dest, fn)]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1548 self.subprocess_check_call(cmd)
38 07849bf248e3 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767 fubar parents: 37 diff changeset	1549 cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest]
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1550 self.subprocess_check_call(cmd)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1551
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1552
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1553 def parse_style_conf(item):
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1554 if item.text.lower() in ["false", "true", "yes", "no"]:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1555 return item.text.lower in ("yes", "true")
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1556 else:
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1557 return item.text
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1558
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1559
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1560 if __name__ == "__main__":
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1561 parser = argparse.ArgumentParser(description="", epilog="")
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1562 parser.add_argument("--xml", help="Track Configuration")
46 4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1563 parser.add_argument(
4181e97c70a7 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a fubar parents: 44 diff changeset	1564 "--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: 44 diff changeset	1565 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1566 parser.add_argument("--outdir", help="Output directory", default="out")
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1567 parser.add_argument("--version", "-V", action="version", version=JB2VER)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1568 args = parser.parse_args()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1569 tree = ET.parse(args.xml)
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1570 root = tree.getroot()
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1571
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1572 # This should be done ASAP
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1573 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1574 # Sometimes this comes as `localhost` without a protocol
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1575 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1576 # so we'll prepend `http://` and hope for the best. Requests should
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1577 # be GET and not POST so it should redirect OK
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1578 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1579
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1580 jc = JbrowseConnector(outdir=args.outdir, jbrowse2path=args.jbrowse2path)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1581
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1582 default_session_data = {}
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1583 trackI = 0
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1584 for ass in root.findall("assembly"):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1585 genomes = [
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1586 {
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1587 "path": x.attrib["path"],
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1588 "label": x.attrib["label"].split(" ")[0].replace(",", ""),
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1589 "useuri": x.attrib["useuri"],
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1590 "meta": metadata_from_node(x.find("metadata")),
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1591 }
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1592 for x in ass.findall("metadata/genomes/genome")
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1593 ]
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1594 primaryGenome = jc.process_genomes(genomes)
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1595 if not default_session_data.get(primaryGenome, None):
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1596 default_session_data[primaryGenome] = {
73 3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1597 "tracks": [],
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1598 "style": {},
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1599 "style_labels": {},
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1600 "visibility": {
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1601 "default_on": [],
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1602 "default_off": [],
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1603 },
3b2815efa5d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b361309b05a861da9b64e1324157a8c32767e0bf fubar parents: 72 diff changeset	1604 }
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1605 for track in ass.find("tracks"):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1606 track_conf = {}
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1607 track_conf["trackfiles"] = []
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1608 track_conf["assemblyNames"] = primaryGenome
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1609 is_multi_bigwig = False
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1610 try:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1611 if track.find("options/wiggle/multibigwig") and (
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1612 track.find("options/wiggle/multibigwig").text == "True"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1613 ):
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1614 is_multi_bigwig = True
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1615 multi_bigwig_paths = []
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1616 except KeyError:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1617 pass
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1618
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1619 trackfiles = track.findall("files/trackFile")
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1620 if trackfiles:
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1621 for x in trackfiles:
93 4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1622 track_conf["label"] = "%s_%d" % (
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1623 x.attrib["label"].replace(" ", "_").replace(",", ""),
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1624 trackI,
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4 fubar parents: 92 diff changeset	1625 )
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1626 trackI += 1
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1627 track_conf["useuri"] = x.attrib["useuri"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1628 if is_multi_bigwig:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1629 multi_bigwig_paths.append(
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1630 (
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1631 track_conf["label"],
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1632 track_conf["useuri"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1633 os.path.realpath(x.attrib["path"]),
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1634 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1635 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1636 else:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1637 if trackfiles:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1638 metadata = metadata_from_node(x.find("metadata"))
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1639 track_conf["dataset_id"] = metadata.get(
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1640 "dataset_id", "None"
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1641 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1642 if x.attrib["useuri"].lower() == "yes":
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1643 tfa = (
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1644 x.attrib["path"],
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1645 x.attrib["ext"],
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1646 x.attrib["useuri"],
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1647 track_conf["label"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1648 metadata,
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1649 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1650 else:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1651 tfa = (
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1652 os.path.realpath(x.attrib["path"]),
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1653 x.attrib["ext"],
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1654 x.attrib["useuri"],
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1655 track_conf["label"],
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1656 metadata,
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1657 )
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1658 track_conf["trackfiles"].append(tfa)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1659
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1660 if is_multi_bigwig:
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1661 metadata = metadata_from_node(x.find("metadata"))
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1662
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1663 track_conf["trackfiles"].append(
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1664 (
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1665 multi_bigwig_paths, # Passing an array of paths to represent as one track
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1666 "bigwig_multiple",
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1667 "MultiBigWig", # Giving an hardcoded name for now
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1668 {}, # No metadata for multiple bigwig
17 4c201a3d4755 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66 fubar parents: 15 diff changeset	1669 )
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1670 )
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1671
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1672 track_conf["category"] = track.attrib["cat"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1673 track_conf["format"] = track.attrib["format"]
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1674 track_conf["conf"] = etree_to_dict(track.find("options"))
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1675 keys = jc.process_annotations(track_conf)
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1676 if keys:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1677 for key in keys:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1678 vis = track.attrib.get("visibility", "default_off")
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1679 if not vis:
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1680 vis = "default_off"
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1681 default_session_data[primaryGenome]["visibility"][vis].append(key)
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1682 trakdat = jc.tracksToAdd[primaryGenome]
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1683 stile = {}
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1684 for trak in trakdat:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1685 if trak["trackId"] == key:
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1686 stile = trak.get("style", {})
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1687 if track.find("options/style"):
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1688 supdate = {
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1689 item.tag: parse_style_conf(item)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1690 for item in track.find("options/style")
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1691 }
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1692 stile.update(supdate)
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1693 default_session_data[primaryGenome]["style"][key] = stile
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1694 if track.find("options/style_labels"):
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1695 default_session_data[primaryGenome]["style_labels"][key] = {
85 3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1696 item.tag: parse_style_conf(item)
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1697 for item in track.find("options/style_labels")
3b2ff9864995 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 264a3d6c7a29f396d359f33164ddf2cb1d9903f8-dirty fubar parents: 83 diff changeset	1698 }
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1699 default_session_data[primaryGenome]["tracks"].append(key)
15 cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1700 default_session_data["defaultLocation"] = root.find(
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1701 "metadata/general/defaultLocation"
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1702 ).text
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1703 default_session_data["session_name"] = root.find(
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1704 "metadata/general/session_name"
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1705 ).text
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1706 logging.debug("default_session=%s" % (json.dumps(default_session_data, indent=2)))
34 2893ef33fba9 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd fubar parents: 32 diff changeset	1707 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
15 cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1708 general_data = {
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1709 "analytics": root.find("metadata/general/analytics").text,
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1710 "primary_color": root.find("metadata/general/primary_color").text,
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1711 "secondary_color": root.find("metadata/general/secondary_color").text,
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1712 "tertiary_color": root.find("metadata/general/tertiary_color").text,
23 39b717d934a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty fubar parents: 19 diff changeset	1713 "quaternary_color": root.find("metadata/general/quaternary_color").text,
15 cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1714 "font_size": root.find("metadata/general/font_size").text,
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1715 }
cce8dacb240f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty fubar parents: 14 diff changeset	1716 jc.add_general_configuration(general_data)
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1717 trackconf = jc.config_json.get("tracks", [])
ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1718 for gnome in jc.genome_names:
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1719 gtracks = jc.tracksToAdd[gnome]
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1720 if len(gtracks) > 0:
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1721 logging.debug(
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1722 "for genome %s adding gtracks %s"
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1723 % (gnome, json.dumps(gtracks, indent=2))
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1724 )
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1725 trackconf += gtracks
62 ab0d6782a95f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty fubar parents: 61 diff changeset	1726 jc.config_json["tracks"] = trackconf
68 c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1727 assconf = jc.config_json.get("assemblies", [])
c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1728 assconf += jc.assemblies
c4eb6a85db70 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty fubar parents: 65 diff changeset	1729 jc.config_json["assemblies"] = assconf
89 408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1730 logging.debug(
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1731 "assmeta=%s, first_contigs=%s, assemblies=%s, gnames=%s, trackidlist=%s, tracks=%s"
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1732 % (
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1733 jc.assmeta,
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1734 jc.ass_first_contigs,
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1735 json.dumps(assconf, indent=2),
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1736 jc.genome_names,
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1737 jc.trackIdlist,
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1738 json.dumps(trackconf, indent=2),
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1739 )
408781c080fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11 fubar parents: 85 diff changeset	1740 )
9 a26c41e304c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b fubar parents: 7 diff changeset	1741 jc.write_config()
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1742 jc.add_default_session(default_session_data)
79 14ecbe46ae9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty fubar parents: 78 diff changeset	1743 # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
80 dff27c9f6d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7bb0fa234bdbc42768b30e426472a47b2523297f fubar parents: 79 diff changeset	1744 # jc.add_defsess_to_index(default_session_data)
0 d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty fubar parents: diff changeset	1745 # jc.text_index() not sure what broke here.

Mercurial > repos > fubar > jbrowse2

annotate jbrowse2.py @ 95:a0c848f00363 draft