annotate jbrowse.py @ 28:d0743cb18ed8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
author iuc
date Fri, 22 Feb 2019 03:20:59 -0500
parents 61ce21e36cb5
children 2bb2e07a7a21
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1 #!/usr/bin/env python
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2 import argparse
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3 import binascii
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4 import copy
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5 import datetime
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6 import hashlib
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7 import json
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8 import logging
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9 import os
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10 import shutil
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11 import struct
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12 import subprocess
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13 import tempfile
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14 import xml.etree.ElementTree as ET
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15 from collections import defaultdict
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16
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17 from Bio.Data import CodonTable
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18 logging.basicConfig(level=logging.INFO)
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19 log = logging.getLogger('jbrowse')
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20 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
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21 GALAXY_INFRASTRUCTURE_URL = None
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23
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24 class ColorScaling(object):
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25
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26 COLOR_FUNCTION_TEMPLATE = """
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27 function(feature, variableName, glyphObject, track) {{
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28 var score = {score};
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29 {opacity}
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30 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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31 }}
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32 """
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33
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34 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
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35 function(feature, variableName, glyphObject, track) {{
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36 var search_up = function self(sf, attr){{
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37 if(sf.get(attr) !== undefined){{
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38 return sf.get(attr);
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39 }}
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40 if(sf.parent() === undefined) {{
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41 return;
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42 }}else{{
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43 return self(sf.parent(), attr);
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44 }}
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45 }};
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46
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47 var search_down = function self(sf, attr){{
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48 if(sf.get(attr) !== undefined){{
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49 return sf.get(attr);
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50 }}
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51 if(sf.children() === undefined) {{
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52 return;
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53 }}else{{
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54 var kids = sf.children();
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55 for(var child_idx in kids){{
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56 var x = self(kids[child_idx], attr);
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57 if(x !== undefined){{
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58 return x;
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59 }}
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60 }}
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61 return;
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62 }}
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63 }};
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64
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65 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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66 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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67 {opacity}
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68 if(score === undefined){{ opacity = 1; }}
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69 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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70 var red = parseInt(result[1], 16);
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71 var green = parseInt(result[2], 16);
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72 var blue = parseInt(result[3], 16);
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73 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
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74 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
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75 }}
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76 """
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77
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78 OPACITY_MATH = {
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79 'linear': """
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80 var opacity = (score - ({min})) / (({max}) - ({min}));
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81 """,
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82 'logarithmic': """
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83 var opacity = (score - ({min})) / (({max}) - ({min}));
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84 opacity = Math.log10(opacity) + Math.log10({max});
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85 """,
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86 'blast': """
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87 var opacity = 0;
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88 if(score == 0.0) {{
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89 opacity = 1;
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90 }} else {{
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91 opacity = (20 - Math.log10(score)) / 180;
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92 }}
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93 """
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94 }
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95
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96 BREWER_COLOUR_IDX = 0
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97 BREWER_COLOUR_SCHEMES = [
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98 (166, 206, 227),
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99 (31, 120, 180),
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100 (178, 223, 138),
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101 (51, 160, 44),
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102 (251, 154, 153),
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103 (227, 26, 28),
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104 (253, 191, 111),
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105 (255, 127, 0),
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106 (202, 178, 214),
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107 (106, 61, 154),
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108 (255, 255, 153),
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109 (177, 89, 40),
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110 (228, 26, 28),
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111 (55, 126, 184),
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112 (77, 175, 74),
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113 (152, 78, 163),
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114 (255, 127, 0),
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115 ]
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116
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117 BREWER_DIVERGING_PALLETES = {
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118 'BrBg': ("#543005", "#003c30"),
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119 'PiYg': ("#8e0152", "#276419"),
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120 'PRGn': ("#40004b", "#00441b"),
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121 'PuOr': ("#7f3b08", "#2d004b"),
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122 'RdBu': ("#67001f", "#053061"),
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123 'RdGy': ("#67001f", "#1a1a1a"),
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124 'RdYlBu': ("#a50026", "#313695"),
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125 'RdYlGn': ("#a50026", "#006837"),
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126 'Spectral': ("#9e0142", "#5e4fa2"),
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127 }
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128
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129 def __init__(self):
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130 self.brewer_colour_idx = 0
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131
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132 def rgb_from_hex(self, hexstr):
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133 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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134 return struct.unpack('BBB', binascii.unhexlify(hexstr))
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135
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136 def min_max_gff(self, gff_file):
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137 min_val = None
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138 max_val = None
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139 with open(gff_file, 'r') as handle:
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140 for line in handle:
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141 try:
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142 value = float(line.split('\t')[5])
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143 min_val = min(value, (min_val or value))
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144 max_val = max(value, (max_val or value))
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145
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146 if value < min_val:
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147 min_val = value
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148
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149 if value > max_val:
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150 max_val = value
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151 except Exception:
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152 pass
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153 return min_val, max_val
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154
3
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155 def hex_from_rgb(self, r, g, b):
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156 return '#%02x%02x%02x' % (r, g, b)
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157
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158 def _get_colours(self):
5
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159 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3
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160 self.brewer_colour_idx += 1
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161 return r, g, b
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162
8
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163 def parse_menus(self, track):
12
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164 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
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165
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166 if 'menu' in track['menus']:
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167 menu_list = [track['menus']['menu']]
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168 if isinstance(track['menus']['menu'], list):
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169 menu_list = track['menus']['menu']
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170
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171 for m in menu_list:
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172 tpl = {
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173 'action': m['action'],
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174 'label': m.get('label', '{name}'),
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175 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
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176 }
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177 if 'url' in m:
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178 tpl['url'] = m['url']
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179 if 'content' in m:
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180 tpl['content'] = m['content']
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181 if 'title' in m:
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182 tpl['title'] = m['title']
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183
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184 trackConfig['menuTemplate'].append(tpl)
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185
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186 return trackConfig
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187
3
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188 def parse_colours(self, track, trackFormat, gff3=None):
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189 # Wiggle tracks have a bicolor pallete
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190 trackConfig = {'style': {}}
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191 if trackFormat == 'wiggle':
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192
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193 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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194 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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195
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196 if trackConfig['style']['pos_color'] == '__auto__':
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197 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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198 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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199
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200 # Wiggle tracks can change colour at a specified place
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201 bc_pivot = track['wiggle']['bicolor_pivot']
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202 if bc_pivot not in ('mean', 'zero'):
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203 # The values are either one of those two strings
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204 # or a number
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205 bc_pivot = float(bc_pivot)
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206 trackConfig['bicolor_pivot'] = bc_pivot
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207 elif 'scaling' in track:
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208 if track['scaling']['method'] == 'ignore':
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209 if track['scaling']['scheme']['color'] != '__auto__':
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210 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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211 else:
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212 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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213 else:
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214 # Scored method
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215 algo = track['scaling']['algo']
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216 # linear, logarithmic, blast
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217 scales = track['scaling']['scales']
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218 # type __auto__, manual (min, max)
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219 scheme = track['scaling']['scheme']
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220 # scheme -> (type (opacity), color)
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221 # ==================================
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222 # GENE CALLS OR BLAST
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223 # ==================================
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224 if trackFormat == 'blast':
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225 red, green, blue = self._get_colours()
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226 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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227 'score': "feature._parent.get('score')",
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228 'opacity': self.OPACITY_MATH['blast'],
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229 'red': red,
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230 'green': green,
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231 'blue': blue,
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232 })
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233 trackConfig['style']['color'] = color_function.replace('\n', '')
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234 elif trackFormat == 'gene_calls':
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235 # Default values, based on GFF3 spec
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236 min_val = 0
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237 max_val = 1000
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238 # Get min/max and build a scoring function since JBrowse doesn't
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239 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3
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240 min_val, max_val = self.min_max_gff(gff3)
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241 else:
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242 min_val = scales.get('min', 0)
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243 max_val = scales.get('max', 1000)
3
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244
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245 if scheme['color'] == '__auto__':
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246 user_color = 'undefined'
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247 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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248 elif scheme['color'].startswith('#'):
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249 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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250 auto_color = 'undefined'
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251 else:
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252 user_color = 'undefined'
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253 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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254
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255 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8
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256 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3
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257 'user_spec_color': user_color,
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258 'auto_gen_color': auto_color,
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259 })
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260
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261 trackConfig['style']['color'] = color_function.replace('\n', '')
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262 return trackConfig
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263
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264
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diff changeset
265 def etree_to_dict(t):
25
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266 if t is None:
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267 return {}
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268
3
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269 d = {t.tag: {} if t.attrib else None}
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270 children = list(t)
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271 if children:
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272 dd = defaultdict(list)
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273 for dc in map(etree_to_dict, children):
10
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274 for k, v in dc.items():
3
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275 dd[k].append(v)
10
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276 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3
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277 if t.attrib:
10
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278 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3
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parents: 1
diff changeset
279 if t.text:
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parents: 1
diff changeset
280 text = t.text.strip()
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parents: 1
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281 if children or t.attrib:
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282 if text:
8
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283 d[t.tag]['#text'] = text
3
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parents: 1
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284 else:
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285 d[t.tag] = text
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parents: 1
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286 return d
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287
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288
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289 # score comes from feature._parent.get('score') or feature.get('score')
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290
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291 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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292
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293
17
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294 def metadata_from_node(node):
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295 metadata = {}
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296 try:
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297 if len(node.findall('dataset')) != 1:
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298 # exit early
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299 return metadata
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300 except Exception:
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301 return {}
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302
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303 for (key, value) in node.findall('dataset')[0].attrib.items():
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304 metadata['dataset_%s' % key] = value
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diff changeset
305
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306 for (key, value) in node.findall('history')[0].attrib.items():
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parents: 16
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307 metadata['history_%s' % key] = value
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308
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309 for (key, value) in node.findall('metadata')[0].attrib.items():
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diff changeset
310 metadata['metadata_%s' % key] = value
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parents: 16
diff changeset
311
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312 for (key, value) in node.findall('tool')[0].attrib.items():
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313 metadata['tool_%s' % key] = value
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314
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315 # Additional Mappings applied:
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316 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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317 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
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318 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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319 galaxy=GALAXY_INFRASTRUCTURE_URL,
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parents: 16
diff changeset
320 encoded_hist_id=metadata['history_id'],
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diff changeset
321 hist_name=metadata['history_display_name']
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322 )
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diff changeset
323 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
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diff changeset
324 galaxy=GALAXY_INFRASTRUCTURE_URL,
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diff changeset
325 encoded_id=metadata['dataset_id'],
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diff changeset
326 tool_id=metadata['tool_tool_id'],
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diff changeset
327 tool_version=metadata['tool_tool_version'],
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diff changeset
328 )
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329 return metadata
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330
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diff changeset
331
3
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parents: 1
diff changeset
332 class JbrowseConnector(object):
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parents: 1
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333
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334 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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parents: 1
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335 self.TN_TABLE = {
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parents: 1
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336 'gff3': '--gff',
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parents: 1
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337 'gff': '--gff',
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parents: 1
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338 'bed': '--bed',
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parents: 1
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339 'genbank': '--gbk',
1
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parents: 0
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340 }
3
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parents: 1
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341
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parents: 1
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342 self.cs = ColorScaling()
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parents: 1
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343 self.jbrowse = jbrowse
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parents: 1
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344 self.outdir = outdir
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parents: 1
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345 self.genome_paths = genomes
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parents: 1
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346 self.standalone = standalone
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347 self.gencode = gencode
8
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348 self.tracksToIndex = []
3
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parents: 1
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349
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parents: 1
diff changeset
350 if standalone:
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parents: 1
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351 self.clone_jbrowse(self.jbrowse, self.outdir)
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parents: 1
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352 else:
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parents: 1
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353 try:
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parents: 1
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354 os.makedirs(self.outdir)
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parents: 1
diff changeset
355 except OSError:
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parents: 1
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356 # Ignore if the folder exists
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parents: 1
diff changeset
357 pass
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parents: 1
diff changeset
358
17
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diff changeset
359 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
360 os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
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parents: 16
diff changeset
361 except OSError:
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diff changeset
362 # Ignore if the folder exists
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iuc
parents: 16
diff changeset
363 pass
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diff changeset
364
3
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parents: 1
diff changeset
365 self.process_genomes()
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parents: 1
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366 self.update_gencode()
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367
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diff changeset
368 def update_gencode(self):
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parents: 1
diff changeset
369 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
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parents: 1
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370 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
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parents: 1
diff changeset
371 with open(trackList, 'r') as handle:
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parents: 1
diff changeset
372 trackListData = json.load(handle)
1
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parents: 0
diff changeset
373
3
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parents: 1
diff changeset
374 trackListData['tracks'][0].update({
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parents: 1
diff changeset
375 'codonStarts': table.start_codons,
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iuc
parents: 1
diff changeset
376 'codonStops': table.stop_codons,
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parents: 1
diff changeset
377 'codonTable': table.forward_table,
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parents: 1
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378 })
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parents: 1
diff changeset
379
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parents: 1
diff changeset
380 with open(trackList, 'w') as handle:
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parents: 1
diff changeset
381 json.dump(trackListData, handle, indent=2)
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parents: 1
diff changeset
382
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iuc
parents: 1
diff changeset
383 def subprocess_check_call(self, command):
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iuc
parents: 1
diff changeset
384 log.debug('cd %s && %s', self.outdir, ' '.join(command))
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parents: 1
diff changeset
385 subprocess.check_call(command, cwd=self.outdir)
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parents: 1
diff changeset
386
25
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parents: 24
diff changeset
387 def subprocess_popen(self, command):
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parents: 24
diff changeset
388 log.debug('cd %s && %s', self.outdir, command)
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parents: 24
diff changeset
389 p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
390 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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parents: 24
diff changeset
391 retcode = p.returncode
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iuc
parents: 24
diff changeset
392 if retcode != 0:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
393 log.error('cd %s && %s', self.outdir, command)
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394 log.error(output)
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395 log.error(err)
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396 raise RuntimeError("Command failed with exit code %s" % (retcode))
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397
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398 def _jbrowse_bin(self, command):
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399 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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400
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401 def process_genomes(self):
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402 for genome_node in self.genome_paths:
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403 # 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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404 # easier to write than the alternative / catches any possible
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405 # issues.
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406
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407 # Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse's data dir
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408 local_genome = os.path.realpath('./genome.fasta')
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409 shutil.copy(genome_node['path'], local_genome)
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410
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411 cmd = ['samtools', 'faidx', local_genome]
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412 self.subprocess_check_call(cmd)
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413
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414 self.subprocess_check_call([
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415 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
25
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416 '--trackConfig', json.dumps({'metadata': genome_node['meta']}),
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417 '--indexed_fasta', os.path.realpath(local_genome)])
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diff changeset
418
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419 os.unlink(local_genome)
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420 os.unlink(local_genome + '.fai')
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421
8
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422 def generate_names(self):
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423 # Generate names
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
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424 args = [
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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425 'perl', self._jbrowse_bin('generate-names.pl'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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426 '--hashBits', '16'
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parents: 5
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427 ]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 5
diff changeset
428
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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429 tracks = ','.join(self.tracksToIndex)
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
430 if tracks:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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431 args += ['--tracks', tracks]
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diff changeset
432 else:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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433 # No tracks to index, index only the refseq
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434 args += ['--tracks', 'DNA']
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
435
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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436 self.subprocess_check_call(args)
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437
5
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438 def _add_json(self, json_data):
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diff changeset
439 cmd = [
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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diff changeset
440 '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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diff changeset
441 json.dumps(json_data),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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442 os.path.join('data', 'trackList.json')
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443 ]
3
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444 self.subprocess_check_call(cmd)
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445
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446 def _add_track_json(self, json_data):
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447 if len(json_data) == 0:
3
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448 return
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449
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450 tmp = tempfile.NamedTemporaryFile(delete=False)
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451 json.dump(json_data, tmp)
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452 tmp.close()
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453 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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454 os.path.join('data', 'trackList.json')]
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455 self.subprocess_check_call(cmd)
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456 os.unlink(tmp.name)
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457
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458 def _blastxml_to_gff3(self, xml, min_gap=10):
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459 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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parents: 1
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460 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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461 '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml]
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462 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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463 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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464 gff3_unrebased.close()
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465 return gff3_unrebased.name
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466
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467 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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468 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
0
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diff changeset
469
5
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470 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
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471 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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472 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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473 if blastOpts.get('protein', 'false') == 'true':
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474 cmd.append('--protein2dna')
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475 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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476 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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parents: 1
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477 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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parents: 1
diff changeset
478 gff3_rebased.close()
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479
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480 # Replace original gff3 file
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481 shutil.copy(gff3_rebased.name, gff3)
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482 os.unlink(gff3_rebased.name)
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parents: 1
diff changeset
483
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484 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
3
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parents: 1
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485
25
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486 self._sort_gff(gff3, dest)
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parents: 1
diff changeset
487
25
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diff changeset
488 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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parents: 24
diff changeset
489 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 24
diff changeset
490 "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
491 "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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492 })
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parents: 1
diff changeset
493
25
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diff changeset
494 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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parents: 12
diff changeset
495
25
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diff changeset
496 trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures'
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diff changeset
497 trackData['type'] = 'BlastView/View/Track/CanvasFeatures'
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parents: 24
diff changeset
498
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diff changeset
499 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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500
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parents: 1
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501 os.unlink(gff3)
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iuc
parents: 1
diff changeset
502
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
503 if blastOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
504 self.tracksToIndex.append("%s" % trackData['label'])
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
505
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
506 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
507 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
508 cmd = ['ln', '-s', data, dest]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
509 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
510
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
511 url = os.path.join('raw', trackData['label'] + '.bw')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
512 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
513 "urlTemplate": url,
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
515 "type": "JBrowse/View/Track/Wiggle/Density",
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
516 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
517
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
518 trackData['type'] = wiggleOpts['type']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
519 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
520
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
521 if 'min' in wiggleOpts and 'max' in wiggleOpts:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
522 trackData['min_score'] = wiggleOpts['min']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
523 trackData['max_score'] = wiggleOpts['max']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
524 else:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
525 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
526
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
527 trackData['scale'] = wiggleOpts['scale']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
528
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
529 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
530
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
531 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
532
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
533 urls = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
534 for idx, bw in enumerate(data):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
535 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
536 cmd = ['ln', '-s', bw[1], dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
537 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
538
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
539 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
540
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
541 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
542 "urlTemplates": urls,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
543 "showTooltips": "true",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
544 "storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
545 "type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
546 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
547 if 'XYPlot' in wiggleOpts['type']:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
548 trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
549
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
550 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
551
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
552 if 'min' in wiggleOpts and 'max' in wiggleOpts:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
553 trackData['min_score'] = wiggleOpts['min']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
554 trackData['max_score'] = wiggleOpts['max']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
555 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
556 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
557
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
558 trackData['scale'] = wiggleOpts['scale']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
559
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
560 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
561
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
562 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
563 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
564 cmd = ['ln', '-s', os.path.realpath(data), dest]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
565 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
566
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
567 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
568 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
569
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
570 url = os.path.join('raw', trackData['label'] + '.bam')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
571 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
572 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
573 "type": "JBrowse/View/Track/Alignments2",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
574 "storeClass": "JBrowse/Store/SeqFeature/BAM",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
575 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
576 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
577
14
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
578 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
579 # So remove the default 'feature' value for these bam tracks
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
580 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
581 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
582
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
583 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
584
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
585 if bamOpts.get('auto_snp', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
586 trackData2 = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
587 trackData2.update({
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
588 "type": "JBrowse/View/Track/SNPCoverage",
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
589 "key": trackData['key'] + " - SNPs/Coverage",
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
590 "label": trackData['label'] + "_autosnp",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
591 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
592 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
593 self._add_track_json(trackData2)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
594
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
595 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
596 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
597 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
598 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
599 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
600 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
601 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
602 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
603 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
604
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
605 url = os.path.join('raw', trackData['label'] + '.vcf.gz')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
606 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
607 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
608 "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
609 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
610 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
611 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
612
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
613 def _sort_gff(self, data, dest):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
614
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
615 if not os.path.exists(dest):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
616 # Only index if not already done
28
d0743cb18ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
iuc
parents: 27
diff changeset
617 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
618 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
619
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
620 cmd = ['bgzip', '-f', dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
621 self.subprocess_popen(' '.join(cmd))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
622 cmd = ['tabix', '-f', '-p', 'gff', dest + '.gz']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
623 self.subprocess_popen(' '.join(cmd))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
624
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
625 def add_features(self, data, format, trackData, gffOpts, **kwargs):
13
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
626
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
627 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
628
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
629 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
630
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
631 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
632 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
633 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
634 "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
635 })
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
636
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
637 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
638 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
639
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
640 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
641 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
642 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
643 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
644 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
645
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
646 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
647 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
648 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
649 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
650 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
651 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
652 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
653 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
654 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
655 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
656
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
657 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
658
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
659 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
660 self.tracksToIndex.append("%s" % trackData['label'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
661
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
662 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
663 data = {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
664 "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
665 "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
666 "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
667 "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
668 "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
669 "baseUrl": url
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
670 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
671 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
672
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
673 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
674 data = {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
675 "label": trackData['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
676 "key": trackData['key'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
677 "category": trackData['category'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
678 "type": "JBrowse/View/Track/CanvasFeatures",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
679 "storeClass": "JBrowse/Store/SeqFeature/SPARQL",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
680 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
681 "queryTemplate": query
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
682 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
683 self._add_track_json(data)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
684
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
685 def process_annotations(self, track):
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
686 category = track['category'].replace('__pd__date__pd__', TODAY)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
687 outputTrackConfig = {
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
688 'style': {
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
689 'label': track['style'].get('label', 'description'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
690 'className': track['style'].get('className', 'feature'),
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
691 'description': track['style'].get('description', ''),
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
692 },
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
693 'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
694 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
695 'maxHeight': track['style'].get('maxHeight', '600'),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
696 'category': category,
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
697 }
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
698
16
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parents: 14
diff changeset
699 mapped_chars = {
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
700 '>': '__gt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
701 '<': '__lt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
702 "'": '__sq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
703 '"': '__dq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
704 '[': '__ob__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
705 ']': '__cb__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
706 '{': '__oc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
707 '}': '__cc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
708 '@': '__at__',
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
709 '#': '__pd__',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
710 "": '__cn__'
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
711 }
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
712
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
713 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
714 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
715 for key, value in mapped_chars.items():
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
716 track_human_label = track_human_label.replace(value, key)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
717
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
718 log.info('Processing %s / %s', category, track_human_label)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
719 outputTrackConfig['key'] = track_human_label
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
720 # We add extra data to hash for the case of REST + SPARQL.
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
721 if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']:
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
722 rest_url = track['conf']['options']['url']
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
723 else:
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
724 rest_url = ''
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
725
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
726 # I chose to use track['category'] instead of 'category' here. This
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
727 # is intentional. This way re-running the tool on a different date
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
728 # will not generate different hashes and make comparison of outputs
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
729 # much simpler.
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
730 hashData = [str(dataset_path), track_human_label, track['category'], rest_url]
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
731 hashData = '|'.join(hashData).encode('utf-8')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
732 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
733 outputTrackConfig['metadata'] = extra_metadata
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
734
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
735 # Colour parsing is complex due to different track types having
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
736 # different colour options.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
737 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
738 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
739 for key in colourOptions:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
740 if key == 'style':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
741 for subkey in colourOptions['style']:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
742 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
743 else:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
744 outputTrackConfig[key] = colourOptions[key]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
745
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
746 if 'menus' in track['conf']['options']:
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
747 menus = self.cs.parse_menus(track['conf']['options'])
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
748 outputTrackConfig.update(menus)
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
749
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
750 # import pprint; pprint.pprint(track)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
751 # import sys; sys.exit()
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
752 if dataset_ext in ('gff', 'gff3', 'bed'):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
753 self.add_features(dataset_path, dataset_ext, outputTrackConfig,
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
754 track['conf']['options']['gff'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
755 elif dataset_ext == 'bigwig':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
756 self.add_bigwig(dataset_path, outputTrackConfig,
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
757 track['conf']['options']['wiggle'])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
758 elif dataset_ext == 'bigwig_multiple':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
759 self.add_bigwig_multiple(dataset_path, outputTrackConfig,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
760 track['conf']['options']['wiggle'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
761 elif dataset_ext == 'bam':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
762 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
763 if not isinstance(real_indexes, list):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
764 # <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
765 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
766 # </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
767 #
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
768 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
769 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
770 # becomes a list. Fun!
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
771 real_indexes = [real_indexes]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
772
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
773 self.add_bam(dataset_path, outputTrackConfig,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
774 track['conf']['options']['pileup'],
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
775 bam_index=real_indexes[i])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
776 elif dataset_ext == 'blastxml':
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
777 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
778 elif dataset_ext == 'vcf':
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
779 self.add_vcf(dataset_path, outputTrackConfig)
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
780 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
781 self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
782 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
783 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
784 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
785 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
786 self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
787 else:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
788 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
789
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
790 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
791 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
792
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
793 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
794 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
795 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
796 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
797
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
798 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
799 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
800
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
801 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
802 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
803
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
804 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
805 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
806 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
807
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
808 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
809 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
810 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
811 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
812 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
813 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
814 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
815 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
816 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
817 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
818
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
819 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
820 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
821
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
822 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
823 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
824 "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
825 "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
826 "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
827 "key": "GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
828 "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
829 "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
830 "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
831 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
832 "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
833 "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
834 "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
835 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
836 "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
837 "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
838 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
839 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
840 # 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
841 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
842 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
843 "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
844 "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
845 "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
846 "key": "GCSkew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
847 "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
848 "gcMode": "skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
849 "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
850 "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
851 "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
852 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
853 "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
854 "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
855 "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
856 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
857 "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
858 "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
859 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
860 }
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
861 # 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
862 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
863
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
864 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
865 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
866 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
867 trackListJson.update({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
868 "trackSelector": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
869 "renameFacets": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
870 "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
871 "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
872 "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
873 "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
874 "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
875 "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
876 "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
877 "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
878 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
879 "displayColumns": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
880 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
881 "tool_tool",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
882 "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
883 "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
884 "dataset_size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
885 "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
886 "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
887 "metadata_dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
888 ],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
889 "type": "Faceted",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
890 "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
891 "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
892 "escapeHTMLInData": False
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
893 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
894 "trackMetadata": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
895 "indexFacets": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
896 "category",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
897 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
898 "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
899 "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
900 "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
901 "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
902 "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
903 ]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
904 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
905 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
906 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
907 json.dump(trackListJson, handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
908
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
909 def clone_jbrowse(self, jbrowse_dir, destination):
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
910 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
911 """
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
912 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
913 # unlike copytree
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
914 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
915 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
916 subprocess.check_call(cmd)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
917 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
918 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
919 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
920
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
921 # 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
922 # JBrowse releases come with some broken symlinks
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
923 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
924 log.debug(' '.join(cmd))
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
925 symlinks = subprocess.check_output(cmd)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
926 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
927 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
928 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
929 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
930 pass
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
931
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
932
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
933 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
934 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
935 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
936
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
937 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
938 parser.add_argument('--outdir', help='Output directory', default='out')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
939 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
940 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
941 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
942
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
943 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
944 root = tree.getroot()
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
945
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
946 # This should be done ASAP
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
947 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
948 # Sometimes this comes as `localhost` without a protocol
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
949 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
950 # 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
951 # 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
952 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
953
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
954 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
955 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
956 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
957 genomes=[
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
958 {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
959 'path': os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
960 'meta': metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
961 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
962 for x in root.findall('metadata/genomes/genome')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
963 ],
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
964 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
965 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
966 )
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
967
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
968 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
969 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
970 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
971 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
972 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
973 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
974 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
975 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
976 '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
977 '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
978 '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
979 '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
980 '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
981 '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
982 '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
983 '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
984 '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
985 },
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
986 'plugins': [],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
987 '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
988 }
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
989
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
990 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
991 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
992 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
993 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
994 '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
995 'name': 'GCContent'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
996 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
997
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
998 # 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
999 # 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
1000 # 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
1001 # '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
1002 # 'name': 'Bookmarks'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1003 # })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1004
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1005 # 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
1006 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
1007 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
1008 # 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
1009 # 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
1010 # '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
1011 # '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
1012 # 'name': 'ComboTrackSelector'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1013 # })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1014
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1015 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
1016 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
1017 '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
1018 'name': 'MinimalistTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1019 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1020 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
1021 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
1022 '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
1023 'name': 'DarkTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1024 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1025
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1026 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
1027 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
1028 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
1029 '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
1030 'name': 'BlastView'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1031 })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1032
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1033 for track in root.findall('tracks/track'):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1034 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
1035 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
1036
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1037 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
1038 try:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1039 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
1040 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
1041 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
1042 except KeyError:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1043 pass
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1044
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1045 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
1046 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1047 for x in track.findall('files/trackFile'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1048 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
1049 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
1050 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1051 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1052 metadata = metadata_from_node(x.find('metadata'))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1053
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1054 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1055 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
1056 x.attrib['ext'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1057 x.attrib['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1058 metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1059 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1060 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1061 # 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
1062 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1063 '', # N/A, no path for rest or sparql
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1064 track.attrib['format'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1065 track.find('options/label').text,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1066 {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1067 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1068
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1069 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
1070 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
1071
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1072 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
1073 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
1074 'bigwig_multiple',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1075 '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
1076 {} # 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
1077 ))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1078
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1079 track_conf['category'] = track.attrib['cat']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1080 track_conf['format'] = track.attrib['format']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1081 try:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1082 # Only pertains to gff3 + blastxml. TODO?
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1083 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
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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
1084 except TypeError:
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1085 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1086 pass
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1087 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
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1088 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
1089
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1090 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
1091 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
1092
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1093 jc.add_final_data(extra_data)
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558d652cd681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
iuc
parents: 17
diff changeset
1094 jc.generate_names()