Mercurial > repos > iuc > jbrowse
annotate jbrowse.py @ 44:87dc4ce42281 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
| author | iuc |
|---|---|
| date | Thu, 22 Apr 2021 20:26:48 +0000 |
| parents | 8774b28235bb |
| children | a6e57ff585c0 |
| rev | line source |
|---|---|
|
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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1 #!/usr/bin/env python |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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2 import argparse |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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3 import binascii |
| 3 | 4 import copy |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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5 import datetime |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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6 import hashlib |
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8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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7 import json |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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8 import logging |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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9 import os |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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10 import shutil |
| 3 | 11 import struct |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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12 import subprocess |
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1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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13 import tempfile |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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14 import xml.etree.ElementTree as ET |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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15 from collections import defaultdict |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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16 |
| 3 | 17 from Bio.Data import CodonTable |
| 18 logging.basicConfig(level=logging.INFO) | |
| 19 log = logging.getLogger('jbrowse') | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d") |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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21 GALAXY_INFRASTRUCTURE_URL = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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22 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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23 |
| 3 | 24 class ColorScaling(object): |
| 25 | |
| 26 COLOR_FUNCTION_TEMPLATE = """ | |
| 27 function(feature, variableName, glyphObject, track) {{ | |
| 28 var score = {score}; | |
| 29 {opacity} | |
| 30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; | |
| 31 }} | |
| 32 """ | |
| 33 | |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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34 COLOR_FUNCTION_TEMPLATE_QUAL = r""" |
| 3 | 35 function(feature, variableName, glyphObject, track) {{ |
| 36 var search_up = function self(sf, attr){{ | |
| 37 if(sf.get(attr) !== undefined){{ | |
| 38 return sf.get(attr); | |
| 39 }} | |
| 40 if(sf.parent() === undefined) {{ | |
| 41 return; | |
| 42 }}else{{ | |
| 43 return self(sf.parent(), attr); | |
| 44 }} | |
| 45 }}; | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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46 |
| 3 | 47 var search_down = function self(sf, attr){{ |
| 48 if(sf.get(attr) !== undefined){{ | |
| 49 return sf.get(attr); | |
| 50 }} | |
| 51 if(sf.children() === undefined) {{ | |
| 52 return; | |
| 53 }}else{{ | |
| 54 var kids = sf.children(); | |
| 55 for(var child_idx in kids){{ | |
| 56 var x = self(kids[child_idx], attr); | |
| 57 if(x !== undefined){{ | |
| 58 return x; | |
| 59 }} | |
| 60 }} | |
| 61 return; | |
| 62 }} | |
| 63 }}; | |
| 64 | |
| 65 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color}); | |
| 66 var score = (search_up(feature, 'score') || search_down(feature, 'score')); | |
| 67 {opacity} | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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68 if(score === undefined){{ opacity = 1; }} |
| 3 | 69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color); |
| 70 var red = parseInt(result[1], 16); | |
| 71 var green = parseInt(result[2], 16); | |
| 72 var blue = parseInt(result[3], 16); | |
| 73 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} | |
| 74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; | |
| 75 }} | |
| 76 """ | |
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0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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77 |
| 3 | 78 OPACITY_MATH = { |
| 79 'linear': """ | |
| 80 var opacity = (score - ({min})) / (({max}) - ({min})); | |
| 81 """, | |
| 82 'logarithmic': """ | |
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2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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83 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min})); |
| 3 | 84 """, |
| 85 'blast': """ | |
| 86 var opacity = 0; | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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87 if(score == 0.0) {{ |
| 3 | 88 opacity = 1; |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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89 }} else {{ |
| 3 | 90 opacity = (20 - Math.log10(score)) / 180; |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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91 }} |
| 3 | 92 """ |
| 93 } | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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94 |
| 3 | 95 BREWER_COLOUR_IDX = 0 |
| 96 BREWER_COLOUR_SCHEMES = [ | |
| 97 (166, 206, 227), | |
| 98 (31, 120, 180), | |
| 99 (178, 223, 138), | |
| 100 (51, 160, 44), | |
| 101 (251, 154, 153), | |
| 102 (227, 26, 28), | |
| 103 (253, 191, 111), | |
| 104 (255, 127, 0), | |
| 105 (202, 178, 214), | |
| 106 (106, 61, 154), | |
| 107 (255, 255, 153), | |
| 108 (177, 89, 40), | |
| 109 (228, 26, 28), | |
| 110 (55, 126, 184), | |
| 111 (77, 175, 74), | |
| 112 (152, 78, 163), | |
| 113 (255, 127, 0), | |
| 114 ] | |
| 115 | |
| 116 BREWER_DIVERGING_PALLETES = { | |
| 117 'BrBg': ("#543005", "#003c30"), | |
| 118 'PiYg': ("#8e0152", "#276419"), | |
| 119 'PRGn': ("#40004b", "#00441b"), | |
| 120 'PuOr': ("#7f3b08", "#2d004b"), | |
| 121 'RdBu': ("#67001f", "#053061"), | |
| 122 'RdGy': ("#67001f", "#1a1a1a"), | |
| 123 'RdYlBu': ("#a50026", "#313695"), | |
| 124 'RdYlGn': ("#a50026", "#006837"), | |
| 125 'Spectral': ("#9e0142", "#5e4fa2"), | |
| 126 } | |
| 127 | |
| 128 def __init__(self): | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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129 self.brewer_colour_idx = 0 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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130 |
| 3 | 131 def rgb_from_hex(self, hexstr): |
| 132 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back | |
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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133 return struct.unpack('BBB', binascii.unhexlify(hexstr)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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134 |
| 3 | 135 def min_max_gff(self, gff_file): |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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136 min_val = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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137 max_val = None |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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138 with open(gff_file, 'r') as handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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139 for line in handle: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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140 try: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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141 value = float(line.split('\t')[5]) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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142 min_val = min(value, (min_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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143 max_val = max(value, (max_val or value)) |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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144 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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145 if value < min_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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146 min_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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147 |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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148 if value > max_val: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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149 max_val = value |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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150 except Exception: |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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151 pass |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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152 return min_val, max_val |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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153 |
| 3 | 154 def hex_from_rgb(self, r, g, b): |
| 155 return '#%02x%02x%02x' % (r, g, b) | |
| 156 | |
| 157 def _get_colours(self): | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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158 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)] |
| 3 | 159 self.brewer_colour_idx += 1 |
| 160 return r, g, b | |
| 161 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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162 def parse_menus(self, track): |
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db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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163 trackConfig = {'menuTemplate': [{}, {}, {}, {}]} |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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164 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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165 if 'menu' in track['menus']: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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166 menu_list = [track['menus']['menu']] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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167 if isinstance(track['menus']['menu'], list): |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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168 menu_list = track['menus']['menu'] |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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169 |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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170 for m in menu_list: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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171 tpl = { |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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172 'action': m['action'], |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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173 'label': m.get('label', '{name}'), |
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174 'iconClass': m.get('iconClass', 'dijitIconBookmark'), |
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175 } |
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176 if 'url' in m: |
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177 tpl['url'] = m['url'] |
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178 if 'content' in m: |
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179 tpl['content'] = m['content'] |
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180 if 'title' in m: |
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181 tpl['title'] = m['title'] |
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182 |
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183 trackConfig['menuTemplate'].append(tpl) |
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184 |
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185 return trackConfig |
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186 |
| 3 | 187 def parse_colours(self, track, trackFormat, gff3=None): |
| 188 # Wiggle tracks have a bicolor pallete | |
| 189 trackConfig = {'style': {}} | |
| 190 if trackFormat == 'wiggle': | |
| 191 | |
| 192 trackConfig['style']['pos_color'] = track['wiggle']['color_pos'] | |
| 193 trackConfig['style']['neg_color'] = track['wiggle']['color_neg'] | |
| 194 | |
| 195 if trackConfig['style']['pos_color'] == '__auto__': | |
| 196 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 197 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours()) | |
| 198 | |
| 199 # Wiggle tracks can change colour at a specified place | |
| 200 bc_pivot = track['wiggle']['bicolor_pivot'] | |
| 201 if bc_pivot not in ('mean', 'zero'): | |
| 202 # The values are either one of those two strings | |
| 203 # or a number | |
| 204 bc_pivot = float(bc_pivot) | |
| 205 trackConfig['bicolor_pivot'] = bc_pivot | |
| 206 elif 'scaling' in track: | |
| 207 if track['scaling']['method'] == 'ignore': | |
| 208 if track['scaling']['scheme']['color'] != '__auto__': | |
| 209 trackConfig['style']['color'] = track['scaling']['scheme']['color'] | |
| 210 else: | |
| 211 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours()) | |
| 212 else: | |
| 213 # Scored method | |
| 214 algo = track['scaling']['algo'] | |
| 215 # linear, logarithmic, blast | |
| 216 scales = track['scaling']['scales'] | |
| 217 # type __auto__, manual (min, max) | |
| 218 scheme = track['scaling']['scheme'] | |
| 219 # scheme -> (type (opacity), color) | |
| 220 # ================================== | |
| 221 # GENE CALLS OR BLAST | |
| 222 # ================================== | |
| 223 if trackFormat == 'blast': | |
| 224 red, green, blue = self._get_colours() | |
| 225 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{ | |
| 226 'score': "feature._parent.get('score')", | |
| 227 'opacity': self.OPACITY_MATH['blast'], | |
| 228 'red': red, | |
| 229 'green': green, | |
| 230 'blue': blue, | |
| 231 }) | |
| 232 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 233 elif trackFormat == 'gene_calls': | |
| 234 # Default values, based on GFF3 spec | |
| 235 min_val = 0 | |
| 236 max_val = 1000 | |
| 237 # Get min/max and build a scoring function since JBrowse doesn't | |
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238 if scales['type'] == 'automatic' or scales['type'] == '__auto__': |
| 3 | 239 min_val, max_val = self.min_max_gff(gff3) |
| 240 else: | |
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241 min_val = scales.get('min', 0) |
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242 max_val = scales.get('max', 1000) |
| 3 | 243 |
| 244 if scheme['color'] == '__auto__': | |
| 245 user_color = 'undefined' | |
| 246 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 247 elif scheme['color'].startswith('#'): | |
| 248 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:])) | |
| 249 auto_color = 'undefined' | |
| 250 else: | |
| 251 user_color = 'undefined' | |
| 252 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours()) | |
| 253 | |
| 254 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{ | |
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255 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}), |
| 3 | 256 'user_spec_color': user_color, |
| 257 'auto_gen_color': auto_color, | |
| 258 }) | |
| 259 | |
| 260 trackConfig['style']['color'] = color_function.replace('\n', '') | |
| 261 return trackConfig | |
| 262 | |
| 263 | |
| 264 def etree_to_dict(t): | |
|
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265 if t is None: |
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266 return {} |
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267 |
| 3 | 268 d = {t.tag: {} if t.attrib else None} |
| 269 children = list(t) | |
| 270 if children: | |
| 271 dd = defaultdict(list) | |
| 272 for dc in map(etree_to_dict, children): | |
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273 for k, v in dc.items(): |
| 3 | 274 dd[k].append(v) |
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275 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}} |
| 3 | 276 if t.attrib: |
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277 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items()) |
| 3 | 278 if t.text: |
| 279 text = t.text.strip() | |
| 280 if children or t.attrib: | |
| 281 if text: | |
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282 d[t.tag]['#text'] = text |
| 3 | 283 else: |
| 284 d[t.tag] = text | |
| 285 return d | |
| 286 | |
| 287 | |
| 288 # score comes from feature._parent.get('score') or feature.get('score') | |
| 289 | |
| 290 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) | |
| 291 | |
| 292 | |
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293 def metadata_from_node(node): |
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294 metadata = {} |
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295 try: |
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296 if len(node.findall('dataset')) != 1: |
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297 # exit early |
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298 return metadata |
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299 except Exception: |
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300 return {} |
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301 |
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302 for (key, value) in node.findall('dataset')[0].attrib.items(): |
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303 metadata['dataset_%s' % key] = value |
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304 |
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305 for (key, value) in node.findall('history')[0].attrib.items(): |
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306 metadata['history_%s' % key] = value |
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307 |
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308 for (key, value) in node.findall('metadata')[0].attrib.items(): |
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309 metadata['metadata_%s' % key] = value |
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310 |
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311 for (key, value) in node.findall('tool')[0].attrib.items(): |
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312 metadata['tool_%s' % key] = value |
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313 |
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314 # Additional Mappings applied: |
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315 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext']) |
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316 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email']) |
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317 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( |
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318 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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319 encoded_hist_id=metadata['history_id'], |
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320 hist_name=metadata['history_display_name'] |
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321 ) |
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322 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format( |
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323 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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324 encoded_id=metadata['dataset_id'], |
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325 tool_id=metadata['tool_tool_id'], |
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326 # tool_version=metadata['tool_tool_version'], |
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327 ) |
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328 return metadata |
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329 |
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330 |
| 3 | 331 class JbrowseConnector(object): |
| 332 | |
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333 def __init__(self, jbrowse, outdir, genomes, standalone=None, gencode=1): |
| 3 | 334 self.cs = ColorScaling() |
| 335 self.jbrowse = jbrowse | |
| 336 self.outdir = outdir | |
| 337 self.genome_paths = genomes | |
| 338 self.standalone = standalone | |
| 339 self.gencode = gencode | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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340 self.tracksToIndex = [] |
| 3 | 341 |
|
40
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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342 if standalone == "complete": |
| 3 | 343 self.clone_jbrowse(self.jbrowse, self.outdir) |
|
40
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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344 elif standalone == "minimal": |
|
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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345 self.clone_jbrowse(self.jbrowse, self.outdir, minimal=True) |
| 3 | 346 else: |
| 347 try: | |
| 348 os.makedirs(self.outdir) | |
| 349 except OSError: | |
| 350 # Ignore if the folder exists | |
| 351 pass | |
| 352 | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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353 try: |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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354 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
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355 except OSError: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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356 # Ignore if the folder exists |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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changeset
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357 pass |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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358 |
| 3 | 359 self.process_genomes() |
| 360 self.update_gencode() | |
| 361 | |
| 362 def update_gencode(self): | |
| 363 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)] | |
| 364 trackList = os.path.join(self.outdir, 'data', 'trackList.json') | |
| 365 with open(trackList, 'r') as handle: | |
| 366 trackListData = json.load(handle) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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changeset
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367 |
| 3 | 368 trackListData['tracks'][0].update({ |
| 369 'codonStarts': table.start_codons, | |
| 370 'codonStops': table.stop_codons, | |
| 371 'codonTable': table.forward_table, | |
| 372 }) | |
| 373 | |
| 374 with open(trackList, 'w') as handle: | |
| 375 json.dump(trackListData, handle, indent=2) | |
| 376 | |
|
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0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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377 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"
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378 if output: |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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379 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"
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380 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"
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381 else: |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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382 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"
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383 subprocess.check_call(command, cwd=self.outdir) |
| 3 | 384 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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385 def subprocess_popen(self, command): |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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386 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
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387 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
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388 output, err = p.communicate() |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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389 retcode = p.returncode |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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390 if retcode != 0: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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391 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
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changeset
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392 log.error(output) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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393 log.error(err) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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394 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
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changeset
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395 |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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396 def subprocess_check_output(self, command): |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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397 log.debug('cd %s && %s', self.outdir, ' '.join(command)) |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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398 return subprocess.check_output(command, cwd=self.outdir) |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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399 |
| 3 | 400 def _jbrowse_bin(self, command): |
| 401 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command)) | |
| 402 | |
|
41
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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403 def symlink_or_copy(self, src, dest): |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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404 if 'GALAXY_JBROWSE_SYMLINKS' in os.environ and bool(os.environ['GALAXY_JBROWSE_SYMLINKS']): |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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changeset
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405 cmd = ['ln', '-s', src, dest] |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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changeset
|
406 else: |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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changeset
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407 cmd = ['cp', src, dest] |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents:
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changeset
|
408 |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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409 return self.subprocess_check_call(cmd) |
|
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents:
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changeset
|
410 |
| 3 | 411 def process_genomes(self): |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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changeset
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412 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
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changeset
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413 # 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
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changeset
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414 # 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
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changeset
|
415 # issues. |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
416 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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changeset
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417 # 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
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418 local_genome = os.path.realpath('./genome.fasta') |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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419 shutil.copy(genome_node['path'], local_genome) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
420 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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421 cmd = ['samtools', 'faidx', local_genome] |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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422 self.subprocess_check_call(cmd) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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423 |
| 3 | 424 self.subprocess_check_call([ |
| 425 '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
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426 '--trackConfig', json.dumps({'metadata': genome_node['meta']}), |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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427 '--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
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changeset
|
428 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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429 os.unlink(local_genome) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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430 os.unlink(local_genome + '.fai') |
| 3 | 431 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
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432 def generate_names(self): |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
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433 # Generate names |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
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434 args = [ |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
435 '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
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diff
changeset
|
436 '--hashBits', '16' |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
437 ] |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
438 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
439 tracks = ','.join(self.tracksToIndex) |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
440 if tracks: |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
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441 args += ['--tracks', tracks] |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
442 else: |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
443 # 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
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changeset
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444 args += ['--tracks', 'DNA'] |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
445 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
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446 self.subprocess_check_call(args) |
| 3 | 447 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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448 def _add_json(self, json_data): |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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449 cmd = [ |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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450 'perl', self._jbrowse_bin('add-json.pl'), |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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451 json.dumps(json_data), |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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452 os.path.join('data', 'trackList.json') |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
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453 ] |
| 3 | 454 self.subprocess_check_call(cmd) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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changeset
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455 |
| 3 | 456 def _add_track_json(self, json_data): |
|
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1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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457 if len(json_data) == 0: |
| 3 | 458 return |
| 459 | |
| 460 tmp = tempfile.NamedTemporaryFile(delete=False) | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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461 json.dump(json_data, tmp) |
| 3 | 462 tmp.close() |
| 463 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name, | |
| 464 os.path.join('data', 'trackList.json')] | |
| 465 self.subprocess_check_call(cmd) | |
| 466 os.unlink(tmp.name) | |
| 467 | |
| 468 def _blastxml_to_gff3(self, xml, min_gap=10): | |
| 469 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) | |
| 470 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'), | |
|
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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471 '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml] |
| 3 | 472 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name) |
| 473 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) | |
| 474 gff3_unrebased.close() | |
| 475 return gff3_unrebased.name | |
| 476 | |
| 477 def add_blastxml(self, data, trackData, blastOpts, **kwargs): | |
| 478 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap']) | |
|
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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479 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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480 if 'parent' in blastOpts and blastOpts['parent'] != 'None': |
| 3 | 481 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) |
| 482 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')] | |
| 483 if blastOpts.get('protein', 'false') == 'true': | |
| 484 cmd.append('--protein2dna') | |
| 485 cmd.extend([os.path.realpath(blastOpts['parent']), gff3]) | |
| 486 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name) | |
| 487 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) | |
| 488 gff3_rebased.close() | |
| 489 | |
| 490 # Replace original gff3 file | |
| 491 shutil.copy(gff3_rebased.name, gff3) | |
| 492 os.unlink(gff3_rebased.name) | |
| 493 | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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494 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff') |
| 3 | 495 |
|
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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496 self._sort_gff(gff3, dest) |
| 3 | 497 |
|
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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498 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
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changeset
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499 trackData.update({ |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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500 "urlTemplate": url, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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501 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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502 }) |
| 3 | 503 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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504 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments' |
|
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69c5e9c0add0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
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changeset
|
505 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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506 trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures' |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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507 trackData['type'] = 'BlastView/View/Track/CanvasFeatures' |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
508 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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509 self._add_track_json(trackData) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
510 |
| 3 | 511 os.unlink(gff3) |
| 512 | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
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513 if blastOpts.get('index', 'false') == 'true': |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
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514 self.tracksToIndex.append("%s" % trackData['label']) |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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515 |
| 3 | 516 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs): |
| 517 dest = os.path.join('data', 'raw', trackData['label'] + '.bw') | |
|
41
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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changeset
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518 self.symlink_or_copy(os.path.realpath(data), dest) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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diff
changeset
|
519 |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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diff
changeset
|
520 url = os.path.join('raw', trackData['label'] + '.bw') |
| 3 | 521 trackData.update({ |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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changeset
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522 "urlTemplate": url, |
| 3 | 523 "storeClass": "JBrowse/Store/SeqFeature/BigWig", |
| 524 "type": "JBrowse/View/Track/Wiggle/Density", | |
| 525 }) | |
| 526 | |
| 527 trackData['type'] = wiggleOpts['type'] | |
| 528 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False | |
| 529 | |
| 530 if 'min' in wiggleOpts and 'max' in wiggleOpts: | |
| 531 trackData['min_score'] = wiggleOpts['min'] | |
| 532 trackData['max_score'] = wiggleOpts['max'] | |
| 533 else: | |
| 534 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') | |
| 535 | |
|
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ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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536 trackData['scale'] = wiggleOpts['scale'] |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
537 |
| 3 | 538 self._add_track_json(trackData) |
| 539 | |
|
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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540 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
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changeset
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541 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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542 urls = [] |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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543 for idx, bw in enumerate(data): |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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544 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw') |
|
41
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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545 self.symlink_or_copy(bw[1], dest) |
|
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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546 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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547 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
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changeset
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548 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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549 trackData.update({ |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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550 "urlTemplates": urls, |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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551 "showTooltips": "true", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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552 "storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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553 "type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity", |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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554 }) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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555 if 'XYPlot' in wiggleOpts['type']: |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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556 trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
557 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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558 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
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changeset
|
559 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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560 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
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changeset
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561 trackData['min_score'] = wiggleOpts['min'] |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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562 trackData['max_score'] = wiggleOpts['max'] |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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563 else: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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564 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local') |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
565 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
566 trackData['scale'] = wiggleOpts['scale'] |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
567 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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568 self._add_track_json(trackData) |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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569 |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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570 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"
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571 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"
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572 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
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changeset
|
573 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
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574 tmp1 = tempfile.NamedTemporaryFile(delete=False) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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575 tmp1.close() |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
576 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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diff
changeset
|
577 # Process MAF to bed-like |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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578 cmd = [script, data] |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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579 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
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|
580 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
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581 # Sort / Index it |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
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582 self._sort_bed(tmp1.path, dest) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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|
583 # Cleanup |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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|
584 try: |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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585 os.remove(tmp1.path) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
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586 except OSError: |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
587 pass |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
588 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
|
589 # Construct samples list |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
590 # 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:
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changeset
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591 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:
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diff
changeset
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592 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
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diff
changeset
|
593 ps.wait() |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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diff
changeset
|
594 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:
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diff
changeset
|
595 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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diff
changeset
|
596 trackData.update({ |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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diff
changeset
|
597 "storeClass": "MAFViewer/Store/SeqFeature/MAFTabix", |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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|
598 "type": "MAFViewer/View/Track/MAF", |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
599 "urlTemplate": trackData['label'] + '.txt.gz', |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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changeset
|
600 "samples": samples, |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
601 }) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
602 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
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changeset
|
603 self._add_track_json(trackData) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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|
604 |
| 3 | 605 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): |
| 606 dest = os.path.join('data', 'raw', trackData['label'] + '.bam') | |
|
41
8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
parents:
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diff
changeset
|
607 self.symlink_or_copy(os.path.realpath(data), dest) |
|
44
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
608 if bam_index is not None: |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
609 # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
610 self.subprocess_check_call(['cp', os.path.realpath(bam_index), dest + '.bai']) |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
611 else: |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
612 # Can happen in exotic condition |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
613 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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changeset
|
614 # => no index generated by galaxy, but there might be one next to the symlink target |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
615 # this trick allows to skip the bam sorting made by galaxy if already done outside |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
parents:
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diff
changeset
|
616 if os.path.exists(os.path.realpath(data) + '.bai'): |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
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changeset
|
617 self.symlink_or_copy(os.path.realpath(data) + '.bai', dest) |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
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changeset
|
618 else: |
|
87dc4ce42281
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 00fb3ea114827e72a2ef344f490eb43a672aa492"
iuc
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changeset
|
619 log.warn('Could not find a bam index (.bai file) for %s', data) |
| 3 | 620 |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
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changeset
|
621 url = os.path.join('raw', trackData['label'] + '.bam') |
| 3 | 622 trackData.update({ |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
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changeset
|
623 "urlTemplate": url, |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
624 "type": "JBrowse/View/Track/Alignments2", |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
625 "storeClass": "JBrowse/Store/SeqFeature/BAM", |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
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626 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000') |
| 3 | 627 }) |
| 628 | |
|
14
18be2d72fdee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents:
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diff
changeset
|
629 # 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
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changeset
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630 # 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:
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changeset
|
631 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
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|
632 del trackData['style']['className'] |
|
18be2d72fdee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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|
633 |
| 3 | 634 self._add_track_json(trackData) |
| 635 | |
| 636 if bamOpts.get('auto_snp', 'false') == 'true': | |
| 637 trackData2 = copy.copy(trackData) | |
| 638 trackData2.update({ | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
|
639 "type": "JBrowse/View/Track/SNPCoverage", |
| 3 | 640 "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:
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diff
changeset
|
641 "label": trackData['label'] + "_autosnp", |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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|
642 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000') |
| 3 | 643 }) |
| 644 self._add_track_json(trackData2) | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
645 |
| 3 | 646 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs): |
| 647 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:
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diff
changeset
|
648 # ln? |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
649 cmd = ['ln', '-s', data, dest] |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
650 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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diff
changeset
|
651 cmd = ['bgzip', dest] |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
652 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
653 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:
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diff
changeset
|
654 self.subprocess_check_call(cmd) |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
|
655 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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|
656 url = os.path.join('raw', trackData['label'] + '.vcf.gz') |
| 3 | 657 trackData.update({ |
|
12
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
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changeset
|
658 "urlTemplate": url, |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
659 "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
|
660 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix", |
| 3 | 661 }) |
| 662 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
|
663 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
664 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
|
665 # 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
|
666 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
|
667 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
|
668 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
|
669 |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
670 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
|
671 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
|
672 |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
673 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
|
674 # 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
|
675 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
|
676 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
|
677 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
|
678 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
|
679 |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
680 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
|
681 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
|
682 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
683 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
|
684 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
|
685 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
686 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
|
687 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
688 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
|
689 trackData.update({ |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
690 "urlTemplate": url, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
691 "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
|
692 }) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
693 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
|
694 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
|
695 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
|
696 |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
697 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
|
698 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
|
699 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
|
700 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
|
701 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
|
702 |
|
27
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
25
diff
changeset
|
703 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
|
704 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
|
705 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
|
706 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
|
707 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
|
708 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
|
709 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
|
710 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
|
711 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
|
712 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
|
713 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
714 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
|
715 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
5
diff
changeset
|
716 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
|
717 self.tracksToIndex.append("%s" % trackData['label']) |
| 3 | 718 |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
719 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
|
720 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
|
721 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
722 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
|
723 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
724 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
|
725 trackData.update({ |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
726 "urlTemplate": url, |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
727 "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
|
728 }) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
729 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
730 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
|
731 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
|
732 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
733 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
|
734 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
|
735 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
736 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
|
737 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
|
738 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
|
739 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
|
740 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
|
741 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
|
742 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
|
743 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
|
744 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
|
745 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
|
746 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
747 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
|
748 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
749 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
|
750 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
|
751 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
752 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
|
753 cmd = [ |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
754 '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
|
755 '--genbank', data, |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
756 '--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
|
757 '--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
|
758 ] |
|
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 # 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
|
761 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
|
762 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
|
763 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
764 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
|
765 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
|
766 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
|
767 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
768 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
|
769 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
|
770 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
|
771 # 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
|
772 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
|
773 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
774 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
|
775 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
776 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
|
777 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
|
778 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
|
779 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
780 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
|
781 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
|
782 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
|
783 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
|
784 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
|
785 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
|
786 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
|
787 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
|
788 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
|
789 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
|
790 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
791 cmd += [ |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
792 '--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
|
793 ] |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
794 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
795 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
|
796 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
797 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
|
798 |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents:
31
diff
changeset
|
799 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
|
800 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
|
801 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
802 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
|
803 data = { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
804 "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
|
805 "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
|
806 "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
|
807 "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
|
808 "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
|
809 "baseUrl": url |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
810 } |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
811 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
|
812 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
813 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
|
814 data = { |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
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changeset
|
815 "label": trackData['label'], |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
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diff
changeset
|
816 "key": trackData['key'], |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
817 "category": trackData['category'], |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
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changeset
|
818 "type": "JBrowse/View/Track/CanvasFeatures", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
819 "storeClass": "JBrowse/Store/SeqFeature/SPARQL", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
820 "urlTemplate": url, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
821 "queryTemplate": query |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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|
822 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
823 self._add_track_json(data) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
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|
824 |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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changeset
|
825 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
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diff
changeset
|
826 trackConfigSubDict = outputTrackConfig |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
827 for part in splitKey[:-1]: |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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changeset
|
828 if trackConfigSubDict.get(part) is None: |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
829 trackConfigSubDict[part] = dict() |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
830 trackConfigSubDict = trackConfigSubDict[part] |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
831 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
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parents:
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diff
changeset
|
832 return trackConfigSubDict |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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changeset
|
833 |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
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|
834 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
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diff
changeset
|
835 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
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diff
changeset
|
836 for valType, value in valType2ValDict.items(): |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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changeset
|
837 if valType == "text": |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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changeset
|
838 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
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changeset
|
839 value = value.replace(mapped_char, char) |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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|
840 elif valType == "integer": |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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841 value = int(value) |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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842 elif valType == "float": |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
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|
843 value = float(value) |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
844 else: # boolean |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
845 value = {'true': True, 'false': False}[value] |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
846 return value |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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|
847 |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
848 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
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diff
changeset
|
849 for optKey, optType2ValDict in customTrackConfig.items(): |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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parents:
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diff
changeset
|
850 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
|
851 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
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parents:
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diff
changeset
|
852 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
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diff
changeset
|
853 trackConfigOptionParent[splitKey[-1]] = optVal |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
854 |
| 3 | 855 def process_annotations(self, track): |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
856 category = track['category'].replace('__pd__date__pd__', TODAY) |
| 3 | 857 outputTrackConfig = { |
| 858 'style': { | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff
changeset
|
859 'label': track['style'].get('label', 'description'), |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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|
860 'className': track['style'].get('className', 'feature'), |
| 3 | 861 'description': track['style'].get('description', ''), |
| 862 }, | |
|
17
ff11d442feed
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|
863 'overridePlugins': track['style'].get('overridePlugins', False) == 'True', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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864 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True', |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
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865 'maxHeight': track['style'].get('maxHeight', '600'), |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
866 'category': category, |
| 3 | 867 } |
| 868 | |
|
16
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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|
869 mapped_chars = { |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
870 '>': '__gt__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
871 '<': '__lt__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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diff
changeset
|
872 "'": '__sq__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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|
873 '"': '__dq__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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|
874 '[': '__ob__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
875 ']': '__cb__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
876 '{': '__oc__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
877 '}': '__cc__', |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
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878 '@': '__at__', |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
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|
879 '#': '__pd__', |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
880 "": '__cn__' |
|
16
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
881 } |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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diff
changeset
|
882 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
883 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
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diff
changeset
|
884 # 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
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changeset
|
885 for key, value in mapped_chars.items(): |
|
b5c5470d7c09
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
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changeset
|
886 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
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changeset
|
887 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
888 log.info('Processing %s / %s', category, track_human_label) |
| 3 | 889 outputTrackConfig['key'] = track_human_label |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
890 # 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
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changeset
|
891 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
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changeset
|
892 rest_url = track['conf']['options']['url'] |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
893 else: |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
894 rest_url = '' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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changeset
|
895 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
896 # 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
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diff
changeset
|
897 # 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
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changeset
|
898 # will not generate different hashes and make comparison of outputs |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
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|
899 # much simpler. |
|
25
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
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|
900 hashData = [str(dataset_path), track_human_label, track['category'], rest_url] |
|
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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|
901 hashData = '|'.join(hashData).encode('utf-8') |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
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|
902 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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|
903 outputTrackConfig['metadata'] = extra_metadata |
| 3 | 904 |
| 905 # Colour parsing is complex due to different track types having | |
| 906 # different colour options. | |
| 907 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path) | |
| 908 # This used to be done with a dict.update() call, however that wiped out any previous style settings... | |
| 909 for key in colourOptions: | |
| 910 if key == 'style': | |
| 911 for subkey in colourOptions['style']: | |
| 912 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey] | |
| 913 else: | |
| 914 outputTrackConfig[key] = colourOptions[key] | |
| 915 | |
|
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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changeset
|
916 if 'menus' in track['conf']['options']: |
|
db5fe5a3176a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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diff
changeset
|
917 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
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changeset
|
918 outputTrackConfig.update(menus) |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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changeset
|
919 |
|
31
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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|
920 customTrackConfig = track['conf']['options'].get('custom_config', {}) |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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|
921 if customTrackConfig: |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff
changeset
|
922 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
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|
923 |
|
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
924 # import pprint; pprint.pprint(track) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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|
925 # import sys; sys.exit() |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
926 if dataset_ext in ('gff', 'gff3'): |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
927 self.add_gff(dataset_path, dataset_ext, outputTrackConfig, |
|
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
928 track['conf']['options']['gff']) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
929 elif dataset_ext in ('bed', ): |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
930 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"
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changeset
|
931 track['conf']['options']['gff']) |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
932 elif dataset_ext in ('genbank', ): |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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|
933 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"
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diff
changeset
|
934 track['conf']['options']['gff']) |
| 3 | 935 elif dataset_ext == 'bigwig': |
| 936 self.add_bigwig(dataset_path, outputTrackConfig, | |
|
25
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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|
937 track['conf']['options']['wiggle']) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
938 elif dataset_ext == 'bigwig_multiple': |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff
changeset
|
939 self.add_bigwig_multiple(dataset_path, outputTrackConfig, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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changeset
|
940 track['conf']['options']['wiggle']) |
|
33
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
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diff
changeset
|
941 elif dataset_ext == 'maf': |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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diff
changeset
|
942 self.add_maf(dataset_path, outputTrackConfig, |
|
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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diff
changeset
|
943 track['conf']['options']['maf']) |
| 3 | 944 elif dataset_ext == 'bam': |
| 945 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index'] | |
| 946 if not isinstance(real_indexes, list): | |
| 947 # <bam_indices> | |
| 948 # <bam_index>/path/to/a.bam.bai</bam_index> | |
| 949 # </bam_indices> | |
| 950 # | |
| 951 # The above will result in the 'bam_index' key containing a | |
| 952 # string. If there are two or more indices, the container | |
| 953 # becomes a list. Fun! | |
| 954 real_indexes = [real_indexes] | |
| 955 | |
| 956 self.add_bam(dataset_path, outputTrackConfig, | |
| 957 track['conf']['options']['pileup'], | |
|
25
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents:
24
diff
changeset
|
958 bam_index=real_indexes[i]) |
| 3 | 959 elif dataset_ext == 'blastxml': |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
960 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast']) |
| 3 | 961 elif dataset_ext == 'vcf': |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
962 self.add_vcf(dataset_path, outputTrackConfig) |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents:
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diff
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|
963 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
|
964 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:
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diff
changeset
|
965 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
|
966 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
|
967 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
|
968 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
|
969 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:
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diff
changeset
|
970 else: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
971 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
|
972 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
973 # 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
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parents:
3
diff
changeset
|
974 yield outputTrackConfig['label'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
975 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
976 def add_final_data(self, data): |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
977 viz_data = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
978 if len(data['visibility']['default_on']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
979 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
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diff
changeset
|
980 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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changeset
|
981 if len(data['visibility']['always']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
982 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
983 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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|
984 if len(data['visibility']['force']) > 0: |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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changeset
|
985 viz_data['forceTracks'] = ','.join(data['visibility']['force']) |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
986 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
987 generalData = {} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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|
988 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:
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diff
changeset
|
989 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()} |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
990 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
991 generalData['view'] = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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|
992 'trackPadding': data['general']['trackPadding'] |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents:
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diff
changeset
|
993 } |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
994 generalData['shareLink'] = (data['general']['shareLink'] == 'true') |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff
changeset
|
995 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
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diff
changeset
|
996 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
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diff
changeset
|
997 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
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|
998 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
|
999 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
|
1000 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
|
1001 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1002 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
|
1003 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
|
1004 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1005 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
|
1006 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
|
1007 "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
|
1008 "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
|
1009 "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
|
1010 "key": "GCContentXY", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1011 "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
|
1012 "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
|
1013 "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
|
1014 "metadata": { |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1015 "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
|
1016 "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
|
1017 "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
|
1018 "dataset_size": "", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1019 "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
|
1020 "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
|
1021 "metadata_dbkey": "", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1022 } |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1023 # 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
|
1024 }) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1025 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
|
1026 "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
|
1027 "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
|
1028 "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
|
1029 "key": "GCSkew", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1030 "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
|
1031 "gcMode": "skew", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1032 "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
|
1033 "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
|
1034 "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
|
1035 "metadata": { |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1036 "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
|
1037 "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
|
1038 "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
|
1039 "dataset_size": "", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1040 "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
|
1041 "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
|
1042 "metadata_dbkey": "", |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1043 } |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1044 # 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
|
1045 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1046 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1047 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
|
1048 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
|
1049 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
|
1050 trackListJson.update({ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1051 "trackSelector": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1052 "renameFacets": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1053 "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
|
1054 "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
|
1055 "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
|
1056 "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
|
1057 "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
|
1058 "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
|
1059 "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
|
1060 "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
|
1061 }, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1062 "displayColumns": [ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1063 "key", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1064 "tool_tool", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1065 "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
|
1066 "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
|
1067 "dataset_size", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1068 "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
|
1069 "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
|
1070 "metadata_dbkey", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1071 ], |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1072 "type": "Faceted", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1073 "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
|
1074 "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
|
1075 "escapeHTMLInData": False |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1076 }, |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1077 "trackMetadata": { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1078 "indexFacets": [ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1079 "category", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1080 "key", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1081 "tool_tool_id", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1082 "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
|
1083 "dataset_edam_format", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1084 "history_user_email", |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1085 "history_display_name" |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1086 ] |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1087 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1088 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1089 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:
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diff
changeset
|
1090 json.dump(trackListJson, handle) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1091 |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1092 def clone_jbrowse(self, jbrowse_dir, destination, minimal=False): |
| 3 | 1093 """Clone a JBrowse directory into a destination directory. |
| 1094 """ | |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1095 if minimal: |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
1096 # Should be the absolute minimum required for JBrowse to function. |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1097 interesting = [ |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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changeset
|
1098 'dist', 'img', 'index.html', 'jbrowse.conf', 'jbrowse_conf.json', 'webpack.config.js' |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1099 ] |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
1100 for i in interesting: |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1101 cmd = ['cp', '-r', os.path.join(jbrowse_dir, i), destination] |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1102 self.subprocess_check_call(cmd) |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1103 else: |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
1104 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1105 # unlike copytree |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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changeset
|
1106 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination] |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1107 self.subprocess_check_call(cmd) |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1108 |
| 3 | 1109 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')] |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
1110 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
|
1111 |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
1112 # 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
|
1113 # 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:
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diff
changeset
|
1114 cmd = ['find', destination, '-type', 'l', '-xtype', 'l'] |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1115 symlinks = self.subprocess_check_output(cmd) |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
1116 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1117 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
|
1118 try: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1119 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
|
1120 except OSError: |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1121 pass |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1122 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1123 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1124 if __name__ == '__main__': |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1125 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
|
1126 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
|
1127 |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1128 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
|
1129 parser.add_argument('--outdir', help='Output directory', default='out') |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
1130 parser.add_argument('--standalone', choices=['complete', 'minimal', 'data'], help='Standalone mode includes a copy of JBrowse') |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1131 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
|
1132 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
|
1133 |
| 3 | 1134 tree = ET.parse(args.xml.name) |
| 1135 root = tree.getroot() | |
| 1136 | |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1137 # This should be done ASAP |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1138 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
|
1139 # 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:
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diff
changeset
|
1140 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
|
1141 # 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
|
1142 # 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
|
1143 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
|
1144 |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
1145 jc = JbrowseConnector( |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
1146 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
|
1147 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
|
1148 genomes=[ |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1149 { |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1150 '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:
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diff
changeset
|
1151 '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:
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diff
changeset
|
1152 } |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1153 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:
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diff
changeset
|
1154 ], |
| 3 | 1155 standalone=args.standalone, |
| 1156 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
|
1157 ) |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
1158 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1159 extra_data = { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1160 'visibility': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1161 'default_on': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1162 'default_off': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1163 'force': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1164 'always': [], |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1165 }, |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1166 'general': { |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1167 '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
|
1168 '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
|
1169 '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
|
1170 '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
|
1171 '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
|
1172 '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
|
1173 '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
|
1174 '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
|
1175 '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
|
1176 }, |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1177 'plugins': [], |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1178 '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
|
1179 } |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1180 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1181 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
|
1182 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
|
1183 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
|
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/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
|
1186 'name': 'GCContent' |
|
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 # 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
|
1190 # 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
|
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/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
|
1193 # 'name': 'Bookmarks' |
|
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 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1196 # 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
|
1197 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
|
1198 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
|
1199 # 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
|
1200 # 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
|
1201 # '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
|
1202 # '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
|
1203 # 'name': 'ComboTrackSelector' |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1204 # }) |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1205 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1206 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
|
1207 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
|
1208 '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
|
1209 'name': 'MinimalistTheme' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1210 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1211 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
|
1212 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
|
1213 '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
|
1214 'name': 'DarkTheme' |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1215 }) |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1216 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1217 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
|
1218 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
|
1219 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
|
1220 '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
|
1221 'name': 'BlastView' |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1222 }) |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
1223 |
| 3 | 1224 for track in root.findall('tracks/track'): |
| 1225 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
|
1226 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
|
1227 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1228 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
|
1229 try: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1230 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
|
1231 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
|
1232 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
|
1233 except KeyError: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1234 pass |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1235 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1236 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
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1237 if trackfiles: |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
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1238 for x in track.findall('files/trackFile'): |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1239 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
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1240 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
|
1241 else: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1242 if trackfiles: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1243 metadata = metadata_from_node(x.find('metadata')) |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1244 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1245 track_conf['trackfiles'].append(( |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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24
diff
changeset
|
1246 os.path.realpath(x.attrib['path']), |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
1247 x.attrib['ext'], |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1248 x.attrib['label'], |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1249 metadata |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1250 )) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1251 else: |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
1252 # 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
|
1253 track_conf['trackfiles'].append(( |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
1254 '', # 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:
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diff
changeset
|
1255 track.attrib['format'], |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
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1256 track.find('options/label').text, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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diff
changeset
|
1257 {} |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1258 )) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1259 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1260 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
|
1261 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
|
1262 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
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diff
changeset
|
1263 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
|
1264 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
|
1265 'bigwig_multiple', |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
24
diff
changeset
|
1266 '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
|
1267 {} # 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
|
1268 )) |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
1269 |
| 3 | 1270 track_conf['category'] = track.attrib['cat'] |
| 1271 track_conf['format'] = track.attrib['format'] | |
| 1272 try: | |
| 1273 # Only pertains to gff3 + blastxml. TODO? | |
| 1274 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
|
1275 except TypeError: |
| 3 | 1276 track_conf['style'] = {} |
| 1277 pass | |
| 1278 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
|
1279 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
|
1280 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1281 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
|
1282 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
|
1283 |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
1284 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:
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diff
changeset
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1285 jc.generate_names() |