jbrowse: jbrowse.py annotate

annotate jbrowse.py @ 34:9de82b4963e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"

author	iuc
date	Wed, 11 Sep 2019 09:40:36 -0400
parents	0ae74c70b267
children	17359b808b01

rev	line source
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1 #!/usr/bin/env python
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	2 import argparse
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	3 import binascii
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	4 import copy
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	5 import datetime
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	6 import hashlib
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	7 import json
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	8 import logging
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	9 import os
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	10 import shutil
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	11 import struct
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	12 import subprocess
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	13 import tempfile
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	14 import xml.etree.ElementTree as ET
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	15 from collections import defaultdict
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	16
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	17 from Bio.Data import CodonTable
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	18 logging.basicConfig(level=logging.INFO)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	19 log = logging.getLogger('jbrowse')
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	21 GALAXY_INFRASTRUCTURE_URL = None
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	22
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	23
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	24 class ColorScaling(object):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	25
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	26 COLOR_FUNCTION_TEMPLATE = """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	27 function(feature, variableName, glyphObject, track) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	28 var score = {score};
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	29 {opacity}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	31 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	32 """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	33
22 5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 21 diff changeset	34 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	35 function(feature, variableName, glyphObject, track) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	36 var search_up = function self(sf, attr){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	37 if(sf.get(attr) !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	38 return sf.get(attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	39 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	40 if(sf.parent() === undefined) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	41 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	42 }}else{{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	43 return self(sf.parent(), attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	44 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	45 }};
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	46
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	47 var search_down = function self(sf, attr){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	48 if(sf.get(attr) !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	49 return sf.get(attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	50 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	51 if(sf.children() === undefined) {{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	52 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	53 }}else{{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	54 var kids = sf.children();
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	55 for(var child_idx in kids){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	56 var x = self(kids[child_idx], attr);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	57 if(x !== undefined){{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	58 return x;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	59 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	60 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	61 return;
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	62 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	63 }};
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	64
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	65 var color = ({user_spec_color} \|\| search_up(feature, 'color') \|\| search_down(feature, 'color') \|\| {auto_gen_color});
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	66 var score = (search_up(feature, 'score') \|\| search_down(feature, 'score'));
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	67 {opacity}
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	68 if(score === undefined){{ opacity = 1; }}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	70 var red = parseInt(result[1], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	71 var green = parseInt(result[2], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	72 var blue = parseInt(result[3], 16);
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	73 if(isNaN(opacity) \|\| opacity < 0){{ opacity = 0; }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	75 }}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	76 """
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	77
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	78 OPACITY_MATH = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	79 'linear': """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	80 var opacity = (score - ({min})) / (({max}) - ({min}));
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	81 """,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	82 'logarithmic': """
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	83 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	84 """,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	85 'blast': """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	86 var opacity = 0;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	87 if(score == 0.0) {{
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	88 opacity = 1;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	89 }} else {{
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	90 opacity = (20 - Math.log10(score)) / 180;
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	91 }}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	92 """
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	93 }
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	94
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	95 BREWER_COLOUR_IDX = 0
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	96 BREWER_COLOUR_SCHEMES = [
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	97 (166, 206, 227),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	98 (31, 120, 180),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	99 (178, 223, 138),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	100 (51, 160, 44),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	101 (251, 154, 153),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	102 (227, 26, 28),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	103 (253, 191, 111),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	104 (255, 127, 0),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	105 (202, 178, 214),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	106 (106, 61, 154),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	107 (255, 255, 153),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	108 (177, 89, 40),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	109 (228, 26, 28),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	110 (55, 126, 184),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	111 (77, 175, 74),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	112 (152, 78, 163),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	113 (255, 127, 0),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	114 ]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	115
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	116 BREWER_DIVERGING_PALLETES = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	117 'BrBg': ("#543005", "#003c30"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	118 'PiYg': ("#8e0152", "#276419"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	119 'PRGn': ("#40004b", "#00441b"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	120 'PuOr': ("#7f3b08", "#2d004b"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	121 'RdBu': ("#67001f", "#053061"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	122 'RdGy': ("#67001f", "#1a1a1a"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	123 'RdYlBu': ("#a50026", "#313695"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	124 'RdYlGn': ("#a50026", "#006837"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	125 'Spectral': ("#9e0142", "#5e4fa2"),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	126 }
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	127
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	128 def __init__(self):
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	129 self.brewer_colour_idx = 0
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	130
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	131 def rgb_from_hex(self, hexstr):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	132 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	133 return struct.unpack('BBB', binascii.unhexlify(hexstr))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	134
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	135 def min_max_gff(self, gff_file):
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	136 min_val = None
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	137 max_val = None
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	138 with open(gff_file, 'r') as handle:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	139 for line in handle:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	140 try:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	141 value = float(line.split('\t')[5])
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	142 min_val = min(value, (min_val or value))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	143 max_val = max(value, (max_val or value))
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	144
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	145 if value < min_val:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	146 min_val = value
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	147
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	148 if value > max_val:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	149 max_val = value
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	150 except Exception:
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	151 pass
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	152 return min_val, max_val
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	153
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	154 def hex_from_rgb(self, r, g, b):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	155 return '#%02x%02x%02x' % (r, g, b)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	156
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	157 def _get_colours(self):
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	158 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	159 self.brewer_colour_idx += 1
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	160 return r, g, b
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	161
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	162 def parse_menus(self, track):
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	163 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	164
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	165 if 'menu' in track['menus']:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	166 menu_list = [track['menus']['menu']]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	167 if isinstance(track['menus']['menu'], list):
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	168 menu_list = track['menus']['menu']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	169
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	170 for m in menu_list:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	171 tpl = {
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	172 'action': m['action'],
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	173 'label': m.get('label', '{name}'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	174 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	175 }
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	176 if 'url' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	177 tpl['url'] = m['url']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	178 if 'content' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	179 tpl['content'] = m['content']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	180 if 'title' in m:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	181 tpl['title'] = m['title']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	182
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	183 trackConfig['menuTemplate'].append(tpl)
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	184
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	185 return trackConfig
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	186
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	187 def parse_colours(self, track, trackFormat, gff3=None):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	188 # Wiggle tracks have a bicolor pallete
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	189 trackConfig = {'style': {}}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	190 if trackFormat == 'wiggle':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	191
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	192 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	193 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	194
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	195 if trackConfig['style']['pos_color'] == '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	196 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	197 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	198
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	199 # Wiggle tracks can change colour at a specified place
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	200 bc_pivot = track['wiggle']['bicolor_pivot']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	201 if bc_pivot not in ('mean', 'zero'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	202 # The values are either one of those two strings
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	203 # or a number
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	204 bc_pivot = float(bc_pivot)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	205 trackConfig['bicolor_pivot'] = bc_pivot
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	206 elif 'scaling' in track:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	207 if track['scaling']['method'] == 'ignore':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	208 if track['scaling']['scheme']['color'] != '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	209 trackConfig['style']['color'] = track['scaling']['scheme']['color']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	210 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	211 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	212 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	213 # Scored method
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	214 algo = track['scaling']['algo']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	215 # linear, logarithmic, blast
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	216 scales = track['scaling']['scales']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	217 # type __auto__, manual (min, max)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	218 scheme = track['scaling']['scheme']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	219 # scheme -> (type (opacity), color)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	220 # ==================================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	221 # GENE CALLS OR BLAST
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	222 # ==================================
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	223 if trackFormat == 'blast':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	224 red, green, blue = self._get_colours()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	225 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	226 'score': "feature._parent.get('score')",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	227 'opacity': self.OPACITY_MATH['blast'],
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	228 'red': red,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	229 'green': green,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	230 'blue': blue,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	231 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	232 trackConfig['style']['color'] = color_function.replace('\n', '')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	233 elif trackFormat == 'gene_calls':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	234 # Default values, based on GFF3 spec
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	235 min_val = 0
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	236 max_val = 1000
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	237 # Get min/max and build a scoring function since JBrowse doesn't
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	238 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	239 min_val, max_val = self.min_max_gff(gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	240 else:
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	241 min_val = scales.get('min', 0)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	242 max_val = scales.get('max', 1000)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	243
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	244 if scheme['color'] == '__auto__':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	245 user_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	246 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	247 elif scheme['color'].startswith('#'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	248 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	249 auto_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	250 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	251 user_color = 'undefined'
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	252 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	253
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	254 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	255 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	256 'user_spec_color': user_color,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	257 'auto_gen_color': auto_color,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	258 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	259
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	260 trackConfig['style']['color'] = color_function.replace('\n', '')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	261 return trackConfig
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	262
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	263
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	264 def etree_to_dict(t):
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	265 if t is None:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	266 return {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	267
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	268 d = {t.tag: {} if t.attrib else None}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	269 children = list(t)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	270 if children:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	271 dd = defaultdict(list)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	272 for dc in map(etree_to_dict, children):
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	273 for k, v in dc.items():
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	274 dd[k].append(v)
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	275 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	276 if t.attrib:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	277 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	278 if t.text:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	279 text = t.text.strip()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	280 if children or t.attrib:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	281 if text:
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	282 d[t.tag]['#text'] = text
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	283 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	284 d[t.tag] = text
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	285 return d
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	286
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	287
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	288 # score comes from feature._parent.get('score') or feature.get('score')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	289
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	290 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	291
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	292
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	293 def metadata_from_node(node):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	294 metadata = {}
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	295 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	296 if len(node.findall('dataset')) != 1:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	297 # exit early
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	298 return metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	299 except Exception:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	300 return {}
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	301
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	302 for (key, value) in node.findall('dataset')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	303 metadata['dataset_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	304
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	305 for (key, value) in node.findall('history')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	306 metadata['history_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	307
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	308 for (key, value) in node.findall('metadata')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	309 metadata['metadata_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	310
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	311 for (key, value) in node.findall('tool')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	312 metadata['tool_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	313
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	314 # Additional Mappings applied:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	315 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	316 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	317 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	318 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	319 encoded_hist_id=metadata['history_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	320 hist_name=metadata['history_display_name']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	321 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	322 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	323 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	324 encoded_id=metadata['dataset_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	325 tool_id=metadata['tool_tool_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	326 tool_version=metadata['tool_tool_version'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	327 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	328 return metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	329
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	330
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	331 class JbrowseConnector(object):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	332
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	333 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	334 self.cs = ColorScaling()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	335 self.jbrowse = jbrowse
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	336 self.outdir = outdir
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	337 self.genome_paths = genomes
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	338 self.standalone = standalone
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	339 self.gencode = gencode
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	340 self.tracksToIndex = []
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	341
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	342 if standalone:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	343 self.clone_jbrowse(self.jbrowse, self.outdir)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	344 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	345 try:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	346 os.makedirs(self.outdir)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	347 except OSError:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	348 # Ignore if the folder exists
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	349 pass
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	350
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	351 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	352 os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	353 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	354 # Ignore if the folder exists
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	355 pass
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	356
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	357 self.process_genomes()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	358 self.update_gencode()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	359
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	360 def update_gencode(self):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	361 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	362 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	363 with open(trackList, 'r') as handle:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	364 trackListData = json.load(handle)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	365
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	366 trackListData['tracks'][0].update({
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	367 'codonStarts': table.start_codons,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	368 'codonStops': table.stop_codons,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	369 'codonTable': table.forward_table,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	370 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	371
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	372 with open(trackList, 'w') as handle:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	373 json.dump(trackListData, handle, indent=2)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	374
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	375 def subprocess_check_call(self, command, output=None):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	376 if output:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	377 log.debug('cd %s && %s > %s', self.outdir, ' '.join(command), output)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	378 subprocess.check_call(command, cwd=self.outdir, stdout=output)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	379 else:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	380 log.debug('cd %s && %s', self.outdir, ' '.join(command))
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	381 subprocess.check_call(command, cwd=self.outdir)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	382
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	383 def subprocess_popen(self, command):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	384 log.debug('cd %s && %s', self.outdir, command)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	385 p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	386 output, err = p.communicate()
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	387 retcode = p.returncode
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	388 if retcode != 0:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	389 log.error('cd %s && %s', self.outdir, command)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	390 log.error(output)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	391 log.error(err)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	392 raise RuntimeError("Command failed with exit code %s" % (retcode))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	393
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	394 def _jbrowse_bin(self, command):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	395 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	396
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	397 def process_genomes(self):
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	398 for genome_node in self.genome_paths:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	399 # We only expect one input genome per run. This for loop is just
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	400 # easier to write than the alternative / catches any possible
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	401 # issues.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	402
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	403 # Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse's data dir
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	404 local_genome = os.path.realpath('./genome.fasta')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	405 shutil.copy(genome_node['path'], local_genome)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	406
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	407 cmd = ['samtools', 'faidx', local_genome]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	408 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	409
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	410 self.subprocess_check_call([
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	411 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	412 '--trackConfig', json.dumps({'metadata': genome_node['meta']}),
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	413 '--indexed_fasta', os.path.realpath(local_genome)])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	414
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	415 os.unlink(local_genome)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	416 os.unlink(local_genome + '.fai')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	417
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	418 def generate_names(self):
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	419 # Generate names
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	420 args = [
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	421 'perl', self._jbrowse_bin('generate-names.pl'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	422 '--hashBits', '16'
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	423 ]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	424
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	425 tracks = ','.join(self.tracksToIndex)
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	426 if tracks:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	427 args += ['--tracks', tracks]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	428 else:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	429 # No tracks to index, index only the refseq
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	430 args += ['--tracks', 'DNA']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	431
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	432 self.subprocess_check_call(args)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	433
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	434 def _add_json(self, json_data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	435 cmd = [
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	436 'perl', self._jbrowse_bin('add-json.pl'),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	437 json.dumps(json_data),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	438 os.path.join('data', 'trackList.json')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	439 ]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	440 self.subprocess_check_call(cmd)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	441
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	442 def _add_track_json(self, json_data):
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	443 if len(json_data) == 0:
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	444 return
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	445
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	446 tmp = tempfile.NamedTemporaryFile(delete=False)
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	447 json.dump(json_data, tmp)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	448 tmp.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	449 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	450 os.path.join('data', 'trackList.json')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	451 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	452 os.unlink(tmp.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	453
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	454 def _blastxml_to_gff3(self, xml, min_gap=10):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	455 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	456 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	457 '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml]
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	458 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	459 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	460 gff3_unrebased.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	461 return gff3_unrebased.name
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	462
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	463 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	464 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	465
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	466 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	467 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	468 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	469 if blastOpts.get('protein', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	470 cmd.append('--protein2dna')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	471 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	472 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	473 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	474 gff3_rebased.close()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	475
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	476 # Replace original gff3 file
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	477 shutil.copy(gff3_rebased.name, gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	478 os.unlink(gff3_rebased.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	479
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	480 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	481
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	482 self._sort_gff(gff3, dest)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	483
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	484 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	485 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	486 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	487 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	488 })
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	489
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	490 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	491
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	492 trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	493 trackData['type'] = 'BlastView/View/Track/CanvasFeatures'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	494
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	495 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	496
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	497 os.unlink(gff3)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	498
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	499 if blastOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	500 self.tracksToIndex.append("%s" % trackData['label'])
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	501
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	502 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	503 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	504 cmd = ['ln', '-s', data, dest]
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	505 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	506
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	507 url = os.path.join('raw', trackData['label'] + '.bw')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	508 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	509 "urlTemplate": url,
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	510 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	511 "type": "JBrowse/View/Track/Wiggle/Density",
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	512 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	513
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	514 trackData['type'] = wiggleOpts['type']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	515 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	516
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	517 if 'min' in wiggleOpts and 'max' in wiggleOpts:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	518 trackData['min_score'] = wiggleOpts['min']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	519 trackData['max_score'] = wiggleOpts['max']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	520 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	521 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	522
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	523 trackData['scale'] = wiggleOpts['scale']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	524
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	525 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	526
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	527 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	528
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	529 urls = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	530 for idx, bw in enumerate(data):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	531 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	532 cmd = ['ln', '-s', bw[1], dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	533 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	534
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	535 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	536
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	537 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	538 "urlTemplates": urls,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	539 "showTooltips": "true",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	540 "storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	541 "type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	542 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	543 if 'XYPlot' in wiggleOpts['type']:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	544 trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	545
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	546 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	547
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	548 if 'min' in wiggleOpts and 'max' in wiggleOpts:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	549 trackData['min_score'] = wiggleOpts['min']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	550 trackData['max_score'] = wiggleOpts['max']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	551 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	552 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	553
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	554 trackData['scale'] = wiggleOpts['scale']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	555
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	556 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	557
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	558 def add_maf(self, data, trackData, mafOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	559 script = os.path.realpath(os.path.join(self.jbrowse, 'plugins', 'MAFViewer', 'bin', 'maf2bed.pl'))
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	560 dest = os.path.join('data', 'raw', trackData['label'] + '.txt')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	561
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	562 tmp1 = tempfile.NamedTemporaryFile(delete=False)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	563 tmp1.close()
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	564
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	565 # Process MAF to bed-like
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	566 cmd = [script, data]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	567 self.subprocess_check_call(cmd, output=tmp1.path)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	568
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	569 # Sort / Index it
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	570 self._sort_bed(tmp1.path, dest)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	571 # Cleanup
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	572 try:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	573 os.remove(tmp1.path)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	574 except OSError:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	575 pass
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	576
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	577 # Construct samples list
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	578 # We could get this from galaxy metadata, not sure how easily.
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	579 ps = subprocess.Popen(['grep', '^s [^ ]*', '-o', data], stdout=subprocess.PIPE)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	580 output = subprocess.check_output(('sort', '-u'), stdin=ps.stdout)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	581 ps.wait()
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	582 samples = [x[2:] for x in output]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	583
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	584 trackData.update({
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	585 "storeClass": "MAFViewer/Store/SeqFeature/MAFTabix",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	586 "type": "MAFViewer/View/Track/MAF",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	587 "urlTemplate": trackData['label'] + '.txt.gz',
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	588 "samples": samples,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	589 })
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	590
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	591 self._add_track_json(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	592
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	593 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	594 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	595 cmd = ['ln', '-s', os.path.realpath(data), dest]
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	596 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	597
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	598 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	599 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	600
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	601 url = os.path.join('raw', trackData['label'] + '.bam')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	602 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	603 "urlTemplate": url,
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	604 "type": "JBrowse/View/Track/Alignments2",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	605 "storeClass": "JBrowse/Store/SeqFeature/BAM",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	606 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	607 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	608
14 18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	609 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	610 # So remove the default 'feature' value for these bam tracks
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	611 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	612 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975 iuc parents: 13 diff changeset	613
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	614 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	615
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	616 if bamOpts.get('auto_snp', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	617 trackData2 = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	618 trackData2.update({
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	619 "type": "JBrowse/View/Track/SNPCoverage",
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	620 "key": trackData['key'] + " - SNPs/Coverage",
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	621 "label": trackData['label'] + "_autosnp",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	622 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	623 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	624 self._add_track_json(trackData2)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	625
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	626 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	627 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	628 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	629 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	630 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	631 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	632 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	633 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	634 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	635
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	636 url = os.path.join('raw', trackData['label'] + '.vcf.gz')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	637 trackData.update({
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	638 "urlTemplate": url,
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	639 "type": "JBrowse/View/Track/HTMLVariants",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	640 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	641 })
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	642 self._add_track_json(trackData)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	643
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	644 def _sort_gff(self, data, dest):
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	645 # Only index if not already done
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	646 if not os.path.exists(dest):
28 d0743cb18ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d iuc parents: 27 diff changeset	647 cmd = "gff3sort.pl --precise '%s' \| grep -v \"^$\" > '%s'" % (data, dest)
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	648 self.subprocess_popen(cmd)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	649
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	650 self.subprocess_check_call(['bgzip', '-f', dest])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	651 self.subprocess_check_call(['tabix', '-f', '-p', 'gff', dest + '.gz'])
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	652
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	653 def _sort_bed(self, data, dest):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	654 # Only index if not already done
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	655 if not os.path.exists(dest):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	656 cmd = ['sort', '-k1,1', '-k2,2n', data]
34 9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	657 with open(dest, 'w') as handle:
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908" iuc parents: 33 diff changeset	658 self.subprocess_check_call(cmd, output=handle)
13 69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79 iuc parents: 12 diff changeset	659
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	660 self.subprocess_check_call(['bgzip', '-f', dest])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	661 self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	662
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	663 def add_gff(self, data, format, trackData, gffOpts, **kwargs):
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	664 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	665
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	666 self._sort_gff(data, dest)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	667
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	668 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	669 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	670 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	671 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	672 })
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	673
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	674 if 'match' in gffOpts:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	675 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	676
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	677 trackType = 'JBrowse/View/Track/CanvasFeatures'
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	678 if 'trackType' in gffOpts:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	679 trackType = gffOpts['trackType']
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	680 trackData['type'] = trackType
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	681 trackData['trackType'] = trackType # Probably only used by old jbrowse versions
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	682
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	683 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	684 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	685 trackData['transcriptType'] = gffOpts['transcriptType']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	686 if 'subParts' in gffOpts and gffOpts['subParts']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	687 trackData['subParts'] = gffOpts['subParts']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	688 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	689 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	690 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	691 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	692 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	693
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	694 self._add_track_json(trackData)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	695
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	696 if gffOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	697 self.tracksToIndex.append("%s" % trackData['label'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	698
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	699 def add_bed(self, data, format, trackData, gffOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	700 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.bed')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	701
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	702 self._sort_bed(data, dest)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	703
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	704 url = os.path.join('raw', trackData['label'] + '.bed.gz')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	705 trackData.update({
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	706 "urlTemplate": url,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	707 "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	708 })
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	709
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	710 if 'match' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	711 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	712
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	713 trackType = gffOpts.get('trackType', 'JBrowse/View/Track/CanvasFeatures')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	714 trackData['type'] = trackType
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	715
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	716 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	717 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	718 trackData['transcriptType'] = gffOpts['transcriptType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	719 if 'subParts' in gffOpts and gffOpts['subParts']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	720 trackData['subParts'] = gffOpts['subParts']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	721 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	722 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	723 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	724 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	725 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	726
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	727 self._add_track_json(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	728
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	729 if gffOpts.get('index', 'false') == 'true':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	730 self.tracksToIndex.append("%s" % trackData['label'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	731
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	732 def add_genbank(self, data, format, trackData, gffOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	733 cmd = [
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	734 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	735 '--genbank', data,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	736 '--trackLabel', trackData['label'],
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	737 '--key', trackData['key']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	738 ]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	739
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	740 # className in --clientConfig is ignored, it needs to be set with --className
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	741 if 'className' in trackData['style']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	742 cmd += ['--className', trackData['style']['className']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	743
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	744 config = copy.copy(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	745 clientConfig = trackData['style']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	746 del config['style']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	747
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	748 if 'match' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	749 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	750 if bool(gffOpts['match']):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	751 # Can be empty for CanvasFeatures = will take all by default
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	752 cmd += ['--type', gffOpts['match']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	753
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	754 cmd += ['--clientConfig', json.dumps(clientConfig)]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	755
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	756 trackType = 'JBrowse/View/Track/CanvasFeatures'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	757 if 'trackType' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	758 trackType = gffOpts['trackType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	759
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	760 if trackType == 'JBrowse/View/Track/CanvasFeatures':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	761 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	762 config['transcriptType'] = gffOpts['transcriptType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	763 if 'subParts' in gffOpts and gffOpts['subParts']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	764 config['subParts'] = gffOpts['subParts']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	765 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	766 config['impliedUTRs'] = gffOpts['impliedUTRs']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	767 elif trackType == 'JBrowse/View/Track/HTMLFeatures':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	768 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	769 cmd += ['--type', gffOpts['transcriptType']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	770
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	771 cmd += [
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	772 '--trackType', gffOpts['trackType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	773 ]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	774
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	775 cmd.extend(['--config', json.dumps(config)])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	776
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	777 self.subprocess_check_call(cmd)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	778
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	779 if gffOpts.get('index', 'false') == 'true':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	780 self.tracksToIndex.append("%s" % trackData['label'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	781
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	782 def add_rest(self, url, trackData):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	783 data = {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	784 "label": trackData['label'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	785 "key": trackData['key'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	786 "category": trackData['category'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	787 "type": "JBrowse/View/Track/HTMLFeatures",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	788 "storeClass": "JBrowse/Store/SeqFeature/REST",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	789 "baseUrl": url
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	790 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	791 self._add_track_json(data)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	792
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	793 def add_sparql(self, url, query, trackData):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	794 data = {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	795 "label": trackData['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	796 "key": trackData['key'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	797 "category": trackData['category'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	798 "type": "JBrowse/View/Track/CanvasFeatures",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	799 "storeClass": "JBrowse/Store/SeqFeature/SPARQL",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	800 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	801 "queryTemplate": query
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	802 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	803 self._add_track_json(data)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	804
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	805 def traverse_to_option_parent(self, splitKey, outputTrackConfig):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	806 trackConfigSubDict = outputTrackConfig
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	807 for part in splitKey[:-1]:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	808 if trackConfigSubDict.get(part) is None:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	809 trackConfigSubDict[part] = dict()
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	810 trackConfigSubDict = trackConfigSubDict[part]
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	811 assert isinstance(trackConfigSubDict, dict), 'Config element {} is not a dict'.format(trackConfigSubDict)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	812 return trackConfigSubDict
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	813
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	814 def get_formatted_option(self, valType2ValDict, mapped_chars):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	815 assert isinstance(valType2ValDict, dict) and len(valType2ValDict.items()) == 1
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	816 for valType, value in valType2ValDict.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	817 if valType == "text":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	818 for char, mapped_char in mapped_chars.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	819 value = value.replace(mapped_char, char)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	820 elif valType == "integer":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	821 value = int(value)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	822 elif valType == "float":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	823 value = float(value)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	824 else: # boolean
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	825 value = {'true': True, 'false': False}[value]
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	826 return value
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	827
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	828 def set_custom_track_options(self, customTrackConfig, outputTrackConfig, mapped_chars):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	829 for optKey, optType2ValDict in customTrackConfig.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	830 splitKey = optKey.split('.')
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	831 trackConfigOptionParent = self.traverse_to_option_parent(splitKey, outputTrackConfig)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	832 optVal = self.get_formatted_option(optType2ValDict, mapped_chars)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	833 trackConfigOptionParent[splitKey[-1]] = optVal
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	834
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	835 def process_annotations(self, track):
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	836 category = track['category'].replace('__pd__date__pd__', TODAY)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	837 outputTrackConfig = {
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	838 'style': {
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	839 'label': track['style'].get('label', 'description'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	840 'className': track['style'].get('className', 'feature'),
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	841 'description': track['style'].get('description', ''),
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	842 },
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	843 'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	844 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	845 'maxHeight': track['style'].get('maxHeight', '600'),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	846 'category': category,
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	847 }
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	848
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	849 mapped_chars = {
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	850 '>': '__gt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	851 '<': '__lt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	852 "'": '__sq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	853 '"': '__dq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	854 '[': '__ob__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	855 ']': '__cb__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	856 '{': '__oc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	857 '}': '__cc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	858 '@': '__at__',
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	859 '#': '__pd__',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	860 "": '__cn__'
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	861 }
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	862
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	863 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
16 b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	864 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	865 for key, value in mapped_chars.items():
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	866 track_human_label = track_human_label.replace(value, key)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5 iuc parents: 14 diff changeset	867
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	868 log.info('Processing %s / %s', category, track_human_label)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	869 outputTrackConfig['key'] = track_human_label
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	870 # We add extra data to hash for the case of REST + SPARQL.
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	871 if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	872 rest_url = track['conf']['options']['url']
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	873 else:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	874 rest_url = ''
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	875
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	876 # I chose to use track['category'] instead of 'category' here. This
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	877 # is intentional. This way re-running the tool on a different date
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	878 # will not generate different hashes and make comparison of outputs
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	879 # much simpler.
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	880 hashData = [str(dataset_path), track_human_label, track['category'], rest_url]
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	881 hashData = '\|'.join(hashData).encode('utf-8')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	882 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	883 outputTrackConfig['metadata'] = extra_metadata
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	884
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	885 # Colour parsing is complex due to different track types having
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	886 # different colour options.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	887 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	888 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	889 for key in colourOptions:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	890 if key == 'style':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	891 for subkey in colourOptions['style']:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	892 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	893 else:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	894 outputTrackConfig[key] = colourOptions[key]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	895
12 db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	896 if 'menus' in track['conf']['options']:
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	897 menus = self.cs.parse_menus(track['conf']['options'])
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1 iuc parents: 11 diff changeset	898 outputTrackConfig.update(menus)
8 ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9 iuc parents: 5 diff changeset	899
31 2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	900 customTrackConfig = track['conf']['options'].get('custom_config', {})
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	901 if customTrackConfig:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	902 self.set_custom_track_options(customTrackConfig, outputTrackConfig, mapped_chars)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c iuc parents: 28 diff changeset	903
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	904 # import pprint; pprint.pprint(track)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	905 # import sys; sys.exit()
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	906 if dataset_ext in ('gff', 'gff3'):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	907 self.add_gff(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	908 track['conf']['options']['gff'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	909 elif dataset_ext in ('bed', ):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	910 self.add_bed(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	911 track['conf']['options']['gff'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	912 elif dataset_ext in ('genbank', ):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	913 self.add_genbank(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	914 track['conf']['options']['gff'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	915 elif dataset_ext == 'bigwig':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	916 self.add_bigwig(dataset_path, outputTrackConfig,
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	917 track['conf']['options']['wiggle'])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	918 elif dataset_ext == 'bigwig_multiple':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	919 self.add_bigwig_multiple(dataset_path, outputTrackConfig,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	920 track['conf']['options']['wiggle'])
33 0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	921 elif dataset_ext == 'maf':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	922 self.add_maf(dataset_path, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3" iuc parents: 31 diff changeset	923 track['conf']['options']['maf'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	924 elif dataset_ext == 'bam':
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	925 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	926 if not isinstance(real_indexes, list):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	927 # <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	928 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	929 # </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	930 #
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	931 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	932 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	933 # becomes a list. Fun!
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	934 real_indexes = [real_indexes]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	935
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	936 self.add_bam(dataset_path, outputTrackConfig,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	937 track['conf']['options']['pileup'],
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	938 bam_index=real_indexes[i])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	939 elif dataset_ext == 'blastxml':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	940 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	941 elif dataset_ext == 'vcf':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	942 self.add_vcf(dataset_path, outputTrackConfig)
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	943 elif dataset_ext == 'rest':
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	944 self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	945 elif dataset_ext == 'sparql':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	946 sparql_query = track['conf']['options']['sparql']['query']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	947 for key, value in mapped_chars.items():
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	948 sparql_query = sparql_query.replace(value, key)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	949 self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	950 else:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	951 log.warn('Do not know how to handle %s', dataset_ext)
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	952
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	953 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	954 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	955
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	956 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	957 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	958 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	959 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	960
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	961 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	962 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	963
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	964 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	965 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	966
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	967 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	968 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	969 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	970
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	971 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	972 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	973 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	974 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	975 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	976 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	977 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	978 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	979 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	980 generalData['plugins'] = data['plugins']
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	981
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	982 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	983 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	984
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	985 if 'GCContent' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	986 self._add_track_json({
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	987 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	988 "type": "GCContent/View/Track/GCContentXY",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	989 "label": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	990 "key": "GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	991 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	992 "bicolor_pivot": 0.5,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	993 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	994 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	995 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	996 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	997 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	998 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	999 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1000 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1001 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1002 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1003 # TODO: Expose params for everyone.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1004 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1005 self._add_track_json({
27 61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46 iuc parents: 25 diff changeset	1006 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1007 "type": "GCContent/View/Track/GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1008 "label": "GC skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1009 "key": "GCSkew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1010 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1011 "gcMode": "skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1012 "min_score": -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1013 "bicolor_pivot": 0,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1014 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1015 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1016 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1017 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1018 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1019 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1020 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1021 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1022 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1023 }
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1024 # TODO: Expose params for everyone.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1025 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1026
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1027 if 'ComboTrackSelector' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1028 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1029 trackListJson = json.load(handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1030 trackListJson.update({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1031 "trackSelector": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1032 "renameFacets": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1033 "tool_tool": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1034 "tool_tool_id": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1035 "tool_tool_version": "Tool Version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1036 "dataset_edam_format": "EDAM",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1037 "dataset_size": "Size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1038 "history_display_name": "History Name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1039 "history_user_email": "Owner",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1040 "metadata_dbkey": "Dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1041 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1042 "displayColumns": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1043 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1044 "tool_tool",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1045 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1046 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1047 "dataset_size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1048 "history_display_name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1049 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1050 "metadata_dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1051 ],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1052 "type": "Faceted",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1053 "title": ["Galaxy Metadata"],
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1054 "icon": "https://galaxyproject.org/images/logos/galaxy-icon-square.png",
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1055 "escapeHTMLInData": False
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1056 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1057 "trackMetadata": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1058 "indexFacets": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1059 "category",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1060 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1061 "tool_tool_id",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1062 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1063 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1064 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1065 "history_display_name"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1066 ]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1067 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1068 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1069 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1070 json.dump(trackListJson, handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1071
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1072 def clone_jbrowse(self, jbrowse_dir, destination):
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1073 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1074 """
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1075 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1076 # unlike copytree
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1077 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1078 log.debug(' '.join(cmd))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1079 subprocess.check_call(cmd)
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1080 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1081 log.debug(' '.join(cmd))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1082 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1083
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1084 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1085 # JBrowse releases come with some broken symlinks
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1086 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1087 log.debug(' '.join(cmd))
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1088 symlinks = subprocess.check_output(cmd)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1089 for i in symlinks:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1090 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1091 os.unlink(i)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1092 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1093 pass
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1094
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1095
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1096 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1097 parser = argparse.ArgumentParser(description="", epilog="")
10 1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524 iuc parents: 8 diff changeset	1098 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1099
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1100 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1101 parser.add_argument('--outdir', help='Output directory', default='out')
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1102 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1103 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0")
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1104 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1105
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1106 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1107 root = tree.getroot()
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1108
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1109 # This should be done ASAP
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1110 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1111 # Sometimes this comes as `localhost` without a protocol
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1112 if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1113 # so we'll prepend `http://` and hope for the best. Requests should
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1114 # be GET and not POST so it should redirect OK
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1115 GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1116
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1117 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1118 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1119 outdir=args.outdir,
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1120 genomes=[
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1121 {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1122 'path': os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1123 'meta': metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1124 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1125 for x in root.findall('metadata/genomes/genome')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1126 ],
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1127 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1128 gencode=root.find('metadata/gencode').text
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1129 )
0 2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e iuc parents: diff changeset	1130
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1131 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1132 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1133 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1134 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1135 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1136 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1137 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1138 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1139 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1140 'trackPadding': int(root.find('metadata/general/trackPadding').text),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1141 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1142 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1143 'show_tracklist': root.find('metadata/general/show_tracklist').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1144 'show_nav': root.find('metadata/general/show_nav').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1145 'show_overview': root.find('metadata/general/show_overview').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1146 'show_menu': root.find('metadata/general/show_menu').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1147 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1148 },
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1149 'plugins': [],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1150 'plugins_python': [],
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1151 }
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1152
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1153 plugins = root.find('plugins').attrib
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1154 if plugins['GCContent'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1155 extra_data['plugins_python'].append('GCContent')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1156 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	1157 'location': 'https://cdn.jsdelivr.net/gh/elsiklab/gccontent@5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1158 'name': 'GCContent'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1159 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1160
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1161 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1162 # if plugins['Bookmarks'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1163 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1164 # 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1165 # 'name': 'Bookmarks'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1166 # })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1167
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1168 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1169 if plugins['ComboTrackSelector'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1170 extra_data['plugins_python'].append('ComboTrackSelector')
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1171 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1172 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1173 # 'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1174 # 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1175 # 'name': 'ComboTrackSelector'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1176 # })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1177
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1178 if plugins['theme'] == 'Minimalist':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1179 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	1180 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-minimalist-theme@d698718442da306cf87f033c72ddb745f3077775/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1181 'name': 'MinimalistTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1182 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1183 elif plugins['theme'] == 'Dark':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1184 extra_data['plugins'].append({
24 fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf iuc parents: 22 diff changeset	1185 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-dark-theme@689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1186 'name': 'DarkTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1187 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1188
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1189 if plugins['BlastView'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1190 extra_data['plugins_python'].append('BlastView')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1191 extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1192 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1193 'name': 'BlastView'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1194 })
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1195
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1196 for track in root.findall('tracks/track'):
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1197 track_conf = {}
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1198 track_conf['trackfiles'] = []
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1199
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1200 is_multi_bigwig = False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1201 try:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1202 if track.find('options/wiggle/multibigwig') and (track.find('options/wiggle/multibigwig').text == 'True'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1203 is_multi_bigwig = True
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1204 multi_bigwig_paths = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1205 except KeyError:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1206 pass
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1207
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1208 trackfiles = track.findall('files/trackFile')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1209 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1210 for x in track.findall('files/trackFile'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1211 if is_multi_bigwig:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1212 multi_bigwig_paths.append((x.attrib['label'], os.path.realpath(x.attrib['path'])))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1213 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1214 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1215 metadata = metadata_from_node(x.find('metadata'))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1216
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1217 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1218 os.path.realpath(x.attrib['path']),
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1219 x.attrib['ext'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1220 x.attrib['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1221 metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1222 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1223 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1224 # For tracks without files (rest, sparql)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1225 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1226 '', # N/A, no path for rest or sparql
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1227 track.attrib['format'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1228 track.find('options/label').text,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1229 {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1230 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1231
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1232 if is_multi_bigwig:
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1233 metadata = metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1234
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1235 track_conf['trackfiles'].append((
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1236 multi_bigwig_paths, # Passing an array of paths to represent as one track
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1237 'bigwig_multiple',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1238 'MultiBigWig', # Giving an hardcoded name for now
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1239 {} # No metadata for multiple bigwig
17 ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257 iuc parents: 16 diff changeset	1240 ))
1 497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f iuc parents: 0 diff changeset	1241
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1242 track_conf['category'] = track.attrib['cat']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1243 track_conf['format'] = track.attrib['format']
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1244 try:
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1245 # Only pertains to gff3 + blastxml. TODO?
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1246 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
25 1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f iuc parents: 24 diff changeset	1247 except TypeError:
3 7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1248 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1249 pass
7342f467507b Uploaded v0.4 of JBrowse iuc parents: 1 diff changeset	1250 track_conf['conf'] = etree_to_dict(track.find('options'))
5 ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1251 keys = jc.process_annotations(track_conf)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1252
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1253 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1254 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1255
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed iuc parents: 3 diff changeset	1256 jc.add_final_data(extra_data)
20 558d652cd681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02 iuc parents: 17 diff changeset	1257 jc.generate_names()

Mercurial > repos > iuc > jbrowse

annotate jbrowse.py @ 34:9de82b4963e6 draft