annotate jbrowse.py @ 34:9de82b4963e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
author iuc
date Wed, 11 Sep 2019 09:40:36 -0400
parents 0ae74c70b267
children 17359b808b01
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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 = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
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84 """,
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85 'blast': """
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86 var opacity = 0;
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87 if(score == 0.0) {{
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88 opacity = 1;
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89 }} else {{
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90 opacity = (20 - Math.log10(score)) / 180;
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91 }}
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92 """
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93 }
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94
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95 BREWER_COLOUR_IDX = 0
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96 BREWER_COLOUR_SCHEMES = [
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97 (166, 206, 227),
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98 (31, 120, 180),
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99 (178, 223, 138),
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100 (51, 160, 44),
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101 (251, 154, 153),
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102 (227, 26, 28),
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103 (253, 191, 111),
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104 (255, 127, 0),
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105 (202, 178, 214),
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106 (106, 61, 154),
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107 (255, 255, 153),
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108 (177, 89, 40),
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109 (228, 26, 28),
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110 (55, 126, 184),
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111 (77, 175, 74),
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112 (152, 78, 163),
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113 (255, 127, 0),
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114 ]
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115
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116 BREWER_DIVERGING_PALLETES = {
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117 'BrBg': ("#543005", "#003c30"),
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118 'PiYg': ("#8e0152", "#276419"),
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119 'PRGn': ("#40004b", "#00441b"),
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120 'PuOr': ("#7f3b08", "#2d004b"),
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121 'RdBu': ("#67001f", "#053061"),
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122 'RdGy': ("#67001f", "#1a1a1a"),
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123 'RdYlBu': ("#a50026", "#313695"),
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124 'RdYlGn': ("#a50026", "#006837"),
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125 'Spectral': ("#9e0142", "#5e4fa2"),
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126 }
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127
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128 def __init__(self):
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129 self.brewer_colour_idx = 0
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130
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131 def rgb_from_hex(self, hexstr):
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132 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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133 return struct.unpack('BBB', binascii.unhexlify(hexstr))
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134
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135 def min_max_gff(self, gff_file):
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136 min_val = None
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137 max_val = None
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138 with open(gff_file, 'r') as handle:
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139 for line in handle:
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140 try:
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141 value = float(line.split('\t')[5])
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142 min_val = min(value, (min_val or value))
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143 max_val = max(value, (max_val or value))
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144
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145 if value < min_val:
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146 min_val = value
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147
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148 if value > max_val:
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149 max_val = value
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150 except Exception:
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151 pass
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152 return min_val, max_val
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153
3
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154 def hex_from_rgb(self, r, g, b):
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155 return '#%02x%02x%02x' % (r, g, b)
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156
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157 def _get_colours(self):
5
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158 r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]
3
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159 self.brewer_colour_idx += 1
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160 return r, g, b
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161
8
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162 def parse_menus(self, track):
12
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163 trackConfig = {'menuTemplate': [{}, {}, {}, {}]}
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164
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165 if 'menu' in track['menus']:
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166 menu_list = [track['menus']['menu']]
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167 if isinstance(track['menus']['menu'], list):
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168 menu_list = track['menus']['menu']
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169
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170 for m in menu_list:
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171 tpl = {
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172 'action': m['action'],
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173 'label': m.get('label', '{name}'),
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174 'iconClass': m.get('iconClass', 'dijitIconBookmark'),
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175 }
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176 if 'url' in m:
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177 tpl['url'] = m['url']
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178 if 'content' in m:
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179 tpl['content'] = m['content']
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180 if 'title' in m:
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181 tpl['title'] = m['title']
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182
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183 trackConfig['menuTemplate'].append(tpl)
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184
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185 return trackConfig
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186
3
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187 def parse_colours(self, track, trackFormat, gff3=None):
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188 # Wiggle tracks have a bicolor pallete
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189 trackConfig = {'style': {}}
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190 if trackFormat == 'wiggle':
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191
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192 trackConfig['style']['pos_color'] = track['wiggle']['color_pos']
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193 trackConfig['style']['neg_color'] = track['wiggle']['color_neg']
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194
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195 if trackConfig['style']['pos_color'] == '__auto__':
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196 trackConfig['style']['neg_color'] = self.hex_from_rgb(*self._get_colours())
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197 trackConfig['style']['pos_color'] = self.hex_from_rgb(*self._get_colours())
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198
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199 # Wiggle tracks can change colour at a specified place
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200 bc_pivot = track['wiggle']['bicolor_pivot']
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201 if bc_pivot not in ('mean', 'zero'):
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202 # The values are either one of those two strings
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203 # or a number
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204 bc_pivot = float(bc_pivot)
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205 trackConfig['bicolor_pivot'] = bc_pivot
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206 elif 'scaling' in track:
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207 if track['scaling']['method'] == 'ignore':
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208 if track['scaling']['scheme']['color'] != '__auto__':
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209 trackConfig['style']['color'] = track['scaling']['scheme']['color']
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210 else:
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211 trackConfig['style']['color'] = self.hex_from_rgb(*self._get_colours())
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212 else:
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213 # Scored method
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214 algo = track['scaling']['algo']
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215 # linear, logarithmic, blast
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216 scales = track['scaling']['scales']
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217 # type __auto__, manual (min, max)
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218 scheme = track['scaling']['scheme']
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219 # scheme -> (type (opacity), color)
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220 # ==================================
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221 # GENE CALLS OR BLAST
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222 # ==================================
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223 if trackFormat == 'blast':
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224 red, green, blue = self._get_colours()
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225 color_function = self.COLOR_FUNCTION_TEMPLATE.format(**{
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226 'score': "feature._parent.get('score')",
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227 'opacity': self.OPACITY_MATH['blast'],
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228 'red': red,
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229 'green': green,
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230 'blue': blue,
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231 })
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232 trackConfig['style']['color'] = color_function.replace('\n', '')
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233 elif trackFormat == 'gene_calls':
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234 # Default values, based on GFF3 spec
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235 min_val = 0
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236 max_val = 1000
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237 # Get min/max and build a scoring function since JBrowse doesn't
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238 if scales['type'] == 'automatic' or scales['type'] == '__auto__':
3
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239 min_val, max_val = self.min_max_gff(gff3)
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240 else:
5
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241 min_val = scales.get('min', 0)
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242 max_val = scales.get('max', 1000)
3
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243
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244 if scheme['color'] == '__auto__':
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245 user_color = 'undefined'
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246 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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247 elif scheme['color'].startswith('#'):
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248 user_color = "'%s'" % self.hex_from_rgb(*self.rgb_from_hex(scheme['color'][1:]))
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249 auto_color = 'undefined'
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250 else:
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251 user_color = 'undefined'
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252 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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253
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254 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(**{
8
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255 'opacity': self.OPACITY_MATH[algo].format(**{'max': max_val, 'min': min_val}),
3
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256 'user_spec_color': user_color,
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257 'auto_gen_color': auto_color,
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258 })
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259
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260 trackConfig['style']['color'] = color_function.replace('\n', '')
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261 return trackConfig
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262
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263
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diff changeset
264 def etree_to_dict(t):
25
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265 if t is None:
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266 return {}
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267
3
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268 d = {t.tag: {} if t.attrib else None}
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269 children = list(t)
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270 if children:
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parents: 1
diff changeset
271 dd = defaultdict(list)
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parents: 1
diff changeset
272 for dc in map(etree_to_dict, children):
10
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iuc
parents: 8
diff changeset
273 for k, v in dc.items():
3
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iuc
parents: 1
diff changeset
274 dd[k].append(v)
10
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parents: 8
diff changeset
275 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
3
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iuc
parents: 1
diff changeset
276 if t.attrib:
10
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iuc
parents: 8
diff changeset
277 d[t.tag].update(('@' + k, v) for k, v in t.attrib.items())
3
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iuc
parents: 1
diff changeset
278 if t.text:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
279 text = t.text.strip()
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iuc
parents: 1
diff changeset
280 if children or t.attrib:
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iuc
parents: 1
diff changeset
281 if text:
8
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iuc
parents: 5
diff changeset
282 d[t.tag]['#text'] = text
3
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iuc
parents: 1
diff changeset
283 else:
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iuc
parents: 1
diff changeset
284 d[t.tag] = text
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iuc
parents: 1
diff changeset
285 return d
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parents: 1
diff changeset
286
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parents: 1
diff changeset
287
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parents: 1
diff changeset
288 # score comes from feature._parent.get('score') or feature.get('score')
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iuc
parents: 1
diff changeset
289
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iuc
parents: 1
diff changeset
290 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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parents: 1
diff changeset
291
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parents: 1
diff changeset
292
17
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iuc
parents: 16
diff changeset
293 def metadata_from_node(node):
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parents: 16
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294 metadata = {}
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parents: 16
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295 try:
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iuc
parents: 16
diff changeset
296 if len(node.findall('dataset')) != 1:
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iuc
parents: 16
diff changeset
297 # exit early
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parents: 16
diff changeset
298 return metadata
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iuc
parents: 16
diff changeset
299 except Exception:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
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300 return {}
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
301
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iuc
parents: 16
diff changeset
302 for (key, value) in node.findall('dataset')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
303 metadata['dataset_%s' % key] = value
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parents: 16
diff changeset
304
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iuc
parents: 16
diff changeset
305 for (key, value) in node.findall('history')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
306 metadata['history_%s' % key] = value
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iuc
parents: 16
diff changeset
307
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
308 for (key, value) in node.findall('metadata')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
309 metadata['metadata_%s' % key] = value
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iuc
parents: 16
diff changeset
310
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
311 for (key, value) in node.findall('tool')[0].attrib.items():
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
312 metadata['tool_%s' % key] = value
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
313
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
314 # Additional Mappings applied:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
315 metadata['dataset_edam_format'] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(metadata['dataset_edam_format'], metadata['dataset_file_ext'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
316 metadata['history_user_email'] = '<a href="mailto:{0}">{0}</a>'.format(metadata['history_user_email'])
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
317 metadata['history_display_name'] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
318 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
319 encoded_hist_id=metadata['history_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
320 hist_name=metadata['history_display_name']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
321 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
322 metadata['tool_tool'] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}</a>'.format(
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
323 galaxy=GALAXY_INFRASTRUCTURE_URL,
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
324 encoded_id=metadata['dataset_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
325 tool_id=metadata['tool_tool_id'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
326 tool_version=metadata['tool_tool_version'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
327 )
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
328 return metadata
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
329
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
330
3
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iuc
parents: 1
diff changeset
331 class JbrowseConnector(object):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
332
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
333 def __init__(self, jbrowse, outdir, genomes, standalone=False, gencode=1):
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iuc
parents: 1
diff changeset
334 self.cs = ColorScaling()
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
335 self.jbrowse = jbrowse
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iuc
parents: 1
diff changeset
336 self.outdir = outdir
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iuc
parents: 1
diff changeset
337 self.genome_paths = genomes
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iuc
parents: 1
diff changeset
338 self.standalone = standalone
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iuc
parents: 1
diff changeset
339 self.gencode = gencode
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
340 self.tracksToIndex = []
3
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iuc
parents: 1
diff changeset
341
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
342 if standalone:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
343 self.clone_jbrowse(self.jbrowse, self.outdir)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
344 else:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
345 try:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
346 os.makedirs(self.outdir)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
347 except OSError:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
348 # Ignore if the folder exists
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
349 pass
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
350
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
351 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
352 os.makedirs(os.path.join(self.outdir, 'data', 'raw'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
353 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
354 # Ignore if the folder exists
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
355 pass
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
356
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
357 self.process_genomes()
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
358 self.update_gencode()
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iuc
parents: 1
diff changeset
359
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
360 def update_gencode(self):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
361 table = CodonTable.unambiguous_dna_by_id[int(self.gencode)]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
362 trackList = os.path.join(self.outdir, 'data', 'trackList.json')
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
363 with open(trackList, 'r') as handle:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
364 trackListData = json.load(handle)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
365
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
366 trackListData['tracks'][0].update({
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
367 'codonStarts': table.start_codons,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
368 'codonStops': table.stop_codons,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
369 'codonTable': table.forward_table,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
370 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
371
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
372 with open(trackList, 'w') as handle:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
373 json.dump(trackListData, handle, indent=2)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
374
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
375 def subprocess_check_call(self, command, output=None):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
376 if output:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
377 log.debug('cd %s && %s > %s', self.outdir, ' '.join(command), output)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
378 subprocess.check_call(command, cwd=self.outdir, stdout=output)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
379 else:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
380 log.debug('cd %s && %s', self.outdir, ' '.join(command))
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
381 subprocess.check_call(command, cwd=self.outdir)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
382
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
383 def subprocess_popen(self, command):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
384 log.debug('cd %s && %s', self.outdir, command)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
385 p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
386 output, err = p.communicate()
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
387 retcode = p.returncode
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388 if retcode != 0:
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389 log.error('cd %s && %s', self.outdir, command)
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390 log.error(output)
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391 log.error(err)
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392 raise RuntimeError("Command failed with exit code %s" % (retcode))
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393
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394 def _jbrowse_bin(self, command):
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395 return os.path.realpath(os.path.join(self.jbrowse, 'bin', command))
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396
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397 def process_genomes(self):
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398 for genome_node in self.genome_paths:
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399 # We only expect one input genome per run. This for loop is just
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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400 # easier to write than the alternative / catches any possible
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401 # issues.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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402
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403 # Copy the file in workdir, prepare-refseqs.pl will copy it to jbrowse's data dir
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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404 local_genome = os.path.realpath('./genome.fasta')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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405 shutil.copy(genome_node['path'], local_genome)
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diff changeset
406
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407 cmd = ['samtools', 'faidx', local_genome]
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408 self.subprocess_check_call(cmd)
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409
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410 self.subprocess_check_call([
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411 'perl', self._jbrowse_bin('prepare-refseqs.pl'),
25
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412 '--trackConfig', json.dumps({'metadata': genome_node['meta']}),
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413 '--indexed_fasta', os.path.realpath(local_genome)])
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diff changeset
414
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415 os.unlink(local_genome)
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416 os.unlink(local_genome + '.fai')
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417
8
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418 def generate_names(self):
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419 # Generate names
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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420 args = [
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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421 'perl', self._jbrowse_bin('generate-names.pl'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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422 '--hashBits', '16'
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423 ]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
424
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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425 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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426 if tracks:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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427 args += ['--tracks', tracks]
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
428 else:
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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429 # No tracks to index, index only the refseq
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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430 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
431
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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432 self.subprocess_check_call(args)
3
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433
5
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434 def _add_json(self, json_data):
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diff changeset
435 cmd = [
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
436 'perl', self._jbrowse_bin('add-json.pl'),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
437 json.dumps(json_data),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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438 os.path.join('data', 'trackList.json')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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439 ]
3
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parents: 1
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440 self.subprocess_check_call(cmd)
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441
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442 def _add_track_json(self, json_data):
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443 if len(json_data) == 0:
3
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444 return
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445
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446 tmp = tempfile.NamedTemporaryFile(delete=False)
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447 json.dump(json_data, tmp)
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448 tmp.close()
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449 cmd = ['perl', self._jbrowse_bin('add-track-json.pl'), tmp.name,
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450 os.path.join('data', 'trackList.json')]
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451 self.subprocess_check_call(cmd)
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452 os.unlink(tmp.name)
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453
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454 def _blastxml_to_gff3(self, xml, min_gap=10):
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455 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
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parents: 1
diff changeset
456 cmd = ['python', os.path.join(INSTALLED_TO, 'blastxml_to_gapped_gff3.py'),
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457 '--trim', '--trim_end', '--include_seq', '--min_gap', str(min_gap), xml]
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458 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_unrebased.name)
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459 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
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460 gff3_unrebased.close()
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461 return gff3_unrebased.name
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parents: 1
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462
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463 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
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464 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts['min_gap'])
0
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diff changeset
465
5
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466 if 'parent' in blastOpts and blastOpts['parent'] != 'None':
3
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467 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
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468 cmd = ['python', os.path.join(INSTALLED_TO, 'gff3_rebase.py')]
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469 if blastOpts.get('protein', 'false') == 'true':
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470 cmd.append('--protein2dna')
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471 cmd.extend([os.path.realpath(blastOpts['parent']), gff3])
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472 log.debug('cd %s && %s > %s', self.outdir, ' '.join(cmd), gff3_rebased.name)
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473 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
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diff changeset
474 gff3_rebased.close()
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475
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parents: 1
diff changeset
476 # Replace original gff3 file
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parents: 1
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477 shutil.copy(gff3_rebased.name, gff3)
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diff changeset
478 os.unlink(gff3_rebased.name)
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parents: 1
diff changeset
479
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diff changeset
480 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
3
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parents: 1
diff changeset
481
25
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482 self._sort_gff(gff3, dest)
3
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parents: 1
diff changeset
483
25
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diff changeset
484 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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parents: 24
diff changeset
485 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
486 "urlTemplate": url,
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
487 "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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diff changeset
488 })
3
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parents: 1
diff changeset
489
25
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diff changeset
490 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
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parents: 12
diff changeset
491
25
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parents: 24
diff changeset
492 trackData['trackType'] = 'BlastView/View/Track/CanvasFeatures'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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diff changeset
493 trackData['type'] = 'BlastView/View/Track/CanvasFeatures'
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parents: 24
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494
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iuc
parents: 24
diff changeset
495 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
496
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
497 os.unlink(gff3)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
498
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
499 if blastOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
500 self.tracksToIndex.append("%s" % trackData['label'])
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
501
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
502 def add_bigwig(self, data, trackData, wiggleOpts, **kwargs):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
503 dest = os.path.join('data', 'raw', trackData['label'] + '.bw')
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
504 cmd = ['ln', '-s', data, dest]
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
505 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
506
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
507 url = os.path.join('raw', trackData['label'] + '.bw')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
508 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
509 "urlTemplate": url,
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
510 "storeClass": "JBrowse/Store/SeqFeature/BigWig",
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
511 "type": "JBrowse/View/Track/Wiggle/Density",
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
512 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
513
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 trackData['type'] = wiggleOpts['type']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
515 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
516
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
517 if 'min' in wiggleOpts and 'max' in wiggleOpts:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
518 trackData['min_score'] = wiggleOpts['min']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
519 trackData['max_score'] = wiggleOpts['max']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
520 else:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
521 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
522
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
523 trackData['scale'] = wiggleOpts['scale']
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
524
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
525 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
526
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
527 def add_bigwig_multiple(self, data, trackData, wiggleOpts, **kwargs):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
528
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
529 urls = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
530 for idx, bw in enumerate(data):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
531 dest = os.path.join('data', 'raw', trackData['label'] + '_' + str(idx) + '.bw')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
532 cmd = ['ln', '-s', bw[1], dest]
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
533 self.subprocess_check_call(cmd)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
534
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
535 urls.append({"url": os.path.join('raw', trackData['label'] + '_' + str(idx) + '.bw'), "name": str(idx + 1) + ' - ' + bw[0]})
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
536
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
537 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
538 "urlTemplates": urls,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
539 "showTooltips": "true",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
540 "storeClass": "MultiBigWig/Store/SeqFeature/MultiBigWig",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
541 "type": "MultiBigWig/View/Track/MultiWiggle/MultiDensity",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
542 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
543 if 'XYPlot' in wiggleOpts['type']:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
544 trackData['type'] = "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
545
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
546 trackData['variance_band'] = True if wiggleOpts['variance_band'] == 'true' else False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
547
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
548 if 'min' in wiggleOpts and 'max' in wiggleOpts:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
549 trackData['min_score'] = wiggleOpts['min']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
550 trackData['max_score'] = wiggleOpts['max']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
551 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
552 trackData['autoscale'] = wiggleOpts.get('autoscale', 'local')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
553
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
554 trackData['scale'] = wiggleOpts['scale']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
555
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
556 self._add_track_json(trackData)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
557
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
558 def add_maf(self, data, trackData, mafOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
559 script = os.path.realpath(os.path.join(self.jbrowse, 'plugins', 'MAFViewer', 'bin', 'maf2bed.pl'))
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
560 dest = os.path.join('data', 'raw', trackData['label'] + '.txt')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
561
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
562 tmp1 = tempfile.NamedTemporaryFile(delete=False)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
563 tmp1.close()
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
564
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
565 # Process MAF to bed-like
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
566 cmd = [script, data]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
567 self.subprocess_check_call(cmd, output=tmp1.path)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
568
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
569 # Sort / Index it
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
570 self._sort_bed(tmp1.path, dest)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
571 # Cleanup
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
572 try:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
573 os.remove(tmp1.path)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
574 except OSError:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
575 pass
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
576
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
577 # Construct samples list
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
578 # We could get this from galaxy metadata, not sure how easily.
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
579 ps = subprocess.Popen(['grep', '^s [^ ]*', '-o', data], stdout=subprocess.PIPE)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
580 output = subprocess.check_output(('sort', '-u'), stdin=ps.stdout)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
581 ps.wait()
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
582 samples = [x[2:] for x in output]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
583
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
584 trackData.update({
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
585 "storeClass": "MAFViewer/Store/SeqFeature/MAFTabix",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
586 "type": "MAFViewer/View/Track/MAF",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
587 "urlTemplate": trackData['label'] + '.txt.gz',
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
588 "samples": samples,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
589 })
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
590
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
591 self._add_track_json(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
592
3
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parents: 1
diff changeset
593 def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
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parents: 1
diff changeset
594 dest = os.path.join('data', 'raw', trackData['label'] + '.bam')
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parents: 1
diff changeset
595 cmd = ['ln', '-s', os.path.realpath(data), dest]
1
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parents: 0
diff changeset
596 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
597
3
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parents: 1
diff changeset
598 cmd = ['ln', '-s', os.path.realpath(bam_index), dest + '.bai']
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iuc
parents: 1
diff changeset
599 self.subprocess_check_call(cmd)
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
600
12
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parents: 11
diff changeset
601 url = os.path.join('raw', trackData['label'] + '.bam')
3
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iuc
parents: 1
diff changeset
602 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
603 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
604 "type": "JBrowse/View/Track/Alignments2",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
605 "storeClass": "JBrowse/Store/SeqFeature/BAM",
25
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iuc
parents: 24
diff changeset
606 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
607 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
608
14
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iuc
parents: 13
diff changeset
609 # Apollo will only switch to the (prettier) 'bam-read' className if it's not set explicitly in the track config
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
610 # So remove the default 'feature' value for these bam tracks
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
611 if 'className' in trackData['style'] and trackData['style']['className'] == 'feature':
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
612 del trackData['style']['className']
18be2d72fdee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 13
diff changeset
613
3
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iuc
parents: 1
diff changeset
614 self._add_track_json(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
615
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
616 if bamOpts.get('auto_snp', 'false') == 'true':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
617 trackData2 = copy.copy(trackData)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
618 trackData2.update({
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
619 "type": "JBrowse/View/Track/SNPCoverage",
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
620 "key": trackData['key'] + " - SNPs/Coverage",
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
621 "label": trackData['label'] + "_autosnp",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
622 "chunkSizeLimit": bamOpts.get('chunkSizeLimit', '5000000')
3
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iuc
parents: 1
diff changeset
623 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
624 self._add_track_json(trackData2)
1
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iuc
parents: 0
diff changeset
625
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
626 def add_vcf(self, data, trackData, vcfOpts={}, **kwargs):
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iuc
parents: 1
diff changeset
627 dest = os.path.join('data', 'raw', trackData['label'] + '.vcf')
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
628 # ln?
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
629 cmd = ['ln', '-s', data, dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
630 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
631 cmd = ['bgzip', dest]
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
632 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
633 cmd = ['tabix', '-p', 'vcf', dest + '.gz']
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
634 self.subprocess_check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
635
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
636 url = os.path.join('raw', trackData['label'] + '.vcf.gz')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
637 trackData.update({
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
638 "urlTemplate": url,
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
639 "type": "JBrowse/View/Track/HTMLVariants",
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
640 "storeClass": "JBrowse/Store/SeqFeature/VCFTabix",
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
641 })
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
642 self._add_track_json(trackData)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
643
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
644 def _sort_gff(self, data, dest):
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
645 # Only index if not already done
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
646 if not os.path.exists(dest):
28
d0743cb18ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3b3c0f1ea1756b0b250b5eb91661f33f11cc9c6d
iuc
parents: 27
diff changeset
647 cmd = "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" % (data, dest)
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
648 self.subprocess_popen(cmd)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
649
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
650 self.subprocess_check_call(['bgzip', '-f', dest])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
651 self.subprocess_check_call(['tabix', '-f', '-p', 'gff', dest + '.gz'])
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
652
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
653 def _sort_bed(self, data, dest):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
654 # Only index if not already done
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
655 if not os.path.exists(dest):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
656 cmd = ['sort', '-k1,1', '-k2,2n', data]
34
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
657 with open(dest, 'w') as handle:
9de82b4963e6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents: 33
diff changeset
658 self.subprocess_check_call(cmd, output=handle)
13
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
659
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
660 self.subprocess_check_call(['bgzip', '-f', dest])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
661 self.subprocess_check_call(['tabix', '-f', '-p', 'bed', dest + '.gz'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
662
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
663 def add_gff(self, data, format, trackData, gffOpts, **kwargs):
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
664 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.gff')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
665
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
666 self._sort_gff(data, dest)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
667
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
668 url = os.path.join('raw', trackData['label'] + '.gff.gz')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
669 trackData.update({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
670 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
671 "storeClass": "JBrowse/Store/SeqFeature/GFF3Tabix",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
672 })
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
673
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
674 if 'match' in gffOpts:
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
675 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
676
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
677 trackType = 'JBrowse/View/Track/CanvasFeatures'
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
678 if 'trackType' in gffOpts:
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
679 trackType = gffOpts['trackType']
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
680 trackData['type'] = trackType
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
681 trackData['trackType'] = trackType # Probably only used by old jbrowse versions
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
682
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
683 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
684 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
685 trackData['transcriptType'] = gffOpts['transcriptType']
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
686 if 'subParts' in gffOpts and gffOpts['subParts']:
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
687 trackData['subParts'] = gffOpts['subParts']
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
688 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
689 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
690 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
691 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
692 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
693
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
694 self._add_track_json(trackData)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
695
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
696 if gffOpts.get('index', 'false') == 'true':
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
697 self.tracksToIndex.append("%s" % trackData['label'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
698
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
699 def add_bed(self, data, format, trackData, gffOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
700 dest = os.path.join(self.outdir, 'data', 'raw', trackData['label'] + '.bed')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
701
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
702 self._sort_bed(data, dest)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
703
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
704 url = os.path.join('raw', trackData['label'] + '.bed.gz')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
705 trackData.update({
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
706 "urlTemplate": url,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
707 "storeClass": "JBrowse/Store/SeqFeature/BEDTabix",
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
708 })
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
709
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
710 if 'match' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
711 trackData['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
712
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
713 trackType = gffOpts.get('trackType', 'JBrowse/View/Track/CanvasFeatures')
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
714 trackData['type'] = trackType
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
715
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
716 if trackType in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
717 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
718 trackData['transcriptType'] = gffOpts['transcriptType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
719 if 'subParts' in gffOpts and gffOpts['subParts']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
720 trackData['subParts'] = gffOpts['subParts']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
721 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
722 trackData['impliedUTRs'] = gffOpts['impliedUTRs']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
723 elif trackType in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
724 if 'topLevelFeatures' in gffOpts and gffOpts['topLevelFeatures']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
725 trackData['topLevelFeatures'] = gffOpts['topLevelFeatures']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
726
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
727 self._add_track_json(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
728
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
729 if gffOpts.get('index', 'false') == 'true':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
730 self.tracksToIndex.append("%s" % trackData['label'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
731
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
732 def add_genbank(self, data, format, trackData, gffOpts, **kwargs):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
733 cmd = [
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
734 'perl', self._jbrowse_bin('flatfile-to-json.pl'),
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
735 '--genbank', data,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
736 '--trackLabel', trackData['label'],
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
737 '--key', trackData['key']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
738 ]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
739
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
740 # className in --clientConfig is ignored, it needs to be set with --className
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
741 if 'className' in trackData['style']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
742 cmd += ['--className', trackData['style']['className']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
743
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
744 config = copy.copy(trackData)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
745 clientConfig = trackData['style']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
746 del config['style']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
747
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
748 if 'match' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
749 config['glyph'] = 'JBrowse/View/FeatureGlyph/Segments'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
750 if bool(gffOpts['match']):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
751 # Can be empty for CanvasFeatures = will take all by default
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
752 cmd += ['--type', gffOpts['match']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
753
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
754 cmd += ['--clientConfig', json.dumps(clientConfig)]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
755
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
756 trackType = 'JBrowse/View/Track/CanvasFeatures'
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
757 if 'trackType' in gffOpts:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
758 trackType = gffOpts['trackType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
759
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
760 if trackType == 'JBrowse/View/Track/CanvasFeatures':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
761 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
762 config['transcriptType'] = gffOpts['transcriptType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
763 if 'subParts' in gffOpts and gffOpts['subParts']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
764 config['subParts'] = gffOpts['subParts']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
765 if 'impliedUTRs' in gffOpts and gffOpts['impliedUTRs']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
766 config['impliedUTRs'] = gffOpts['impliedUTRs']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
767 elif trackType == 'JBrowse/View/Track/HTMLFeatures':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
768 if 'transcriptType' in gffOpts and gffOpts['transcriptType']:
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
769 cmd += ['--type', gffOpts['transcriptType']]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
770
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
771 cmd += [
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
772 '--trackType', gffOpts['trackType']
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
773 ]
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
774
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
775 cmd.extend(['--config', json.dumps(config)])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
776
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
777 self.subprocess_check_call(cmd)
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
778
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
779 if gffOpts.get('index', 'false') == 'true':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
780 self.tracksToIndex.append("%s" % trackData['label'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
781
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
782 def add_rest(self, url, trackData):
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
783 data = {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
784 "label": trackData['label'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
785 "key": trackData['key'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
786 "category": trackData['category'],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
787 "type": "JBrowse/View/Track/HTMLFeatures",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
788 "storeClass": "JBrowse/Store/SeqFeature/REST",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
789 "baseUrl": url
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
790 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
791 self._add_track_json(data)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
792
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
793 def add_sparql(self, url, query, trackData):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
794 data = {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
795 "label": trackData['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
796 "key": trackData['key'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
797 "category": trackData['category'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
798 "type": "JBrowse/View/Track/CanvasFeatures",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
799 "storeClass": "JBrowse/Store/SeqFeature/SPARQL",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
800 "urlTemplate": url,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
801 "queryTemplate": query
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
802 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
803 self._add_track_json(data)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
804
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
805 def traverse_to_option_parent(self, splitKey, outputTrackConfig):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
806 trackConfigSubDict = outputTrackConfig
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
807 for part in splitKey[:-1]:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
808 if trackConfigSubDict.get(part) is None:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
809 trackConfigSubDict[part] = dict()
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
810 trackConfigSubDict = trackConfigSubDict[part]
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
811 assert isinstance(trackConfigSubDict, dict), 'Config element {} is not a dict'.format(trackConfigSubDict)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
812 return trackConfigSubDict
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
813
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
814 def get_formatted_option(self, valType2ValDict, mapped_chars):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
815 assert isinstance(valType2ValDict, dict) and len(valType2ValDict.items()) == 1
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
816 for valType, value in valType2ValDict.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
817 if valType == "text":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
818 for char, mapped_char in mapped_chars.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
819 value = value.replace(mapped_char, char)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
820 elif valType == "integer":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
821 value = int(value)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
822 elif valType == "float":
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
823 value = float(value)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
824 else: # boolean
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
825 value = {'true': True, 'false': False}[value]
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
826 return value
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
827
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
828 def set_custom_track_options(self, customTrackConfig, outputTrackConfig, mapped_chars):
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
829 for optKey, optType2ValDict in customTrackConfig.items():
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
830 splitKey = optKey.split('.')
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
831 trackConfigOptionParent = self.traverse_to_option_parent(splitKey, outputTrackConfig)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
832 optVal = self.get_formatted_option(optType2ValDict, mapped_chars)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
833 trackConfigOptionParent[splitKey[-1]] = optVal
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
834
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
835 def process_annotations(self, track):
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
836 category = track['category'].replace('__pd__date__pd__', TODAY)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
837 outputTrackConfig = {
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
838 'style': {
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
839 'label': track['style'].get('label', 'description'),
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
840 'className': track['style'].get('className', 'feature'),
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
841 'description': track['style'].get('description', ''),
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
842 },
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
843 'overridePlugins': track['style'].get('overridePlugins', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
844 'overrideDraggable': track['style'].get('overrideDraggable', False) == 'True',
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
845 'maxHeight': track['style'].get('maxHeight', '600'),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
846 'category': category,
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
847 }
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
848
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
849 mapped_chars = {
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
850 '>': '__gt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
851 '<': '__lt__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
852 "'": '__sq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
853 '"': '__dq__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
854 '[': '__ob__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
855 ']': '__cb__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
856 '{': '__oc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
857 '}': '__cc__',
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
858 '@': '__at__',
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
859 '#': '__pd__',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
860 "": '__cn__'
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
861 }
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
862
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
863 for i, (dataset_path, dataset_ext, track_human_label, extra_metadata) in enumerate(track['trackfiles']):
16
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
864 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
865 for key, value in mapped_chars.items():
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
866 track_human_label = track_human_label.replace(value, key)
b5c5470d7c09 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
iuc
parents: 14
diff changeset
867
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
868 log.info('Processing %s / %s', category, track_human_label)
3
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iuc
parents: 1
diff changeset
869 outputTrackConfig['key'] = track_human_label
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
870 # We add extra data to hash for the case of REST + SPARQL.
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
871 if 'conf' in track and 'options' in track['conf'] and 'url' in track['conf']['options']:
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
872 rest_url = track['conf']['options']['url']
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
873 else:
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
874 rest_url = ''
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
875
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
876 # I chose to use track['category'] instead of 'category' here. This
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
877 # is intentional. This way re-running the tool on a different date
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
878 # will not generate different hashes and make comparison of outputs
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
879 # much simpler.
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
880 hashData = [str(dataset_path), track_human_label, track['category'], rest_url]
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
881 hashData = '|'.join(hashData).encode('utf-8')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
882 outputTrackConfig['label'] = hashlib.md5(hashData).hexdigest() + '_%s' % i
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
883 outputTrackConfig['metadata'] = extra_metadata
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
884
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
885 # Colour parsing is complex due to different track types having
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
886 # different colour options.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
887 colourOptions = self.cs.parse_colours(track['conf']['options'], track['format'], gff3=dataset_path)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
888 # This used to be done with a dict.update() call, however that wiped out any previous style settings...
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
889 for key in colourOptions:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
890 if key == 'style':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
891 for subkey in colourOptions['style']:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
892 outputTrackConfig['style'][subkey] = colourOptions['style'][subkey]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
893 else:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
894 outputTrackConfig[key] = colourOptions[key]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
895
12
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
896 if 'menus' in track['conf']['options']:
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
897 menus = self.cs.parse_menus(track['conf']['options'])
db5fe5a3176a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 11
diff changeset
898 outputTrackConfig.update(menus)
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 5
diff changeset
899
31
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
900 customTrackConfig = track['conf']['options'].get('custom_config', {})
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
901 if customTrackConfig:
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
902 self.set_custom_track_options(customTrackConfig, outputTrackConfig, mapped_chars)
2bb2e07a7a21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents: 28
diff changeset
903
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
904 # import pprint; pprint.pprint(track)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
905 # import sys; sys.exit()
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
906 if dataset_ext in ('gff', 'gff3'):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
907 self.add_gff(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
908 track['conf']['options']['gff'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
909 elif dataset_ext in ('bed', ):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
910 self.add_bed(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
911 track['conf']['options']['gff'])
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
912 elif dataset_ext in ('genbank', ):
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
913 self.add_genbank(dataset_path, dataset_ext, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
914 track['conf']['options']['gff'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
915 elif dataset_ext == 'bigwig':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
916 self.add_bigwig(dataset_path, outputTrackConfig,
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
917 track['conf']['options']['wiggle'])
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
918 elif dataset_ext == 'bigwig_multiple':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
919 self.add_bigwig_multiple(dataset_path, outputTrackConfig,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
920 track['conf']['options']['wiggle'])
33
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
921 elif dataset_ext == 'maf':
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
922 self.add_maf(dataset_path, outputTrackConfig,
0ae74c70b267 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
parents: 31
diff changeset
923 track['conf']['options']['maf'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
924 elif dataset_ext == 'bam':
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
925 real_indexes = track['conf']['options']['pileup']['bam_indices']['bam_index']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
926 if not isinstance(real_indexes, list):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
927 # <bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
928 # <bam_index>/path/to/a.bam.bai</bam_index>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
929 # </bam_indices>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
930 #
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
931 # The above will result in the 'bam_index' key containing a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
932 # string. If there are two or more indices, the container
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
933 # becomes a list. Fun!
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
934 real_indexes = [real_indexes]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
935
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
936 self.add_bam(dataset_path, outputTrackConfig,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
937 track['conf']['options']['pileup'],
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
938 bam_index=real_indexes[i])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
939 elif dataset_ext == 'blastxml':
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
940 self.add_blastxml(dataset_path, outputTrackConfig, track['conf']['options']['blast'])
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
941 elif dataset_ext == 'vcf':
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
942 self.add_vcf(dataset_path, outputTrackConfig)
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
943 elif dataset_ext == 'rest':
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
944 self.add_rest(track['conf']['options']['rest']['url'], outputTrackConfig)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
945 elif dataset_ext == 'sparql':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
946 sparql_query = track['conf']['options']['sparql']['query']
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
947 for key, value in mapped_chars.items():
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
948 sparql_query = sparql_query.replace(value, key)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
949 self.add_sparql(track['conf']['options']['sparql']['url'], sparql_query, outputTrackConfig)
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
950 else:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
951 log.warn('Do not know how to handle %s', dataset_ext)
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
952
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
953 # Return non-human label for use in other fields
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
954 yield outputTrackConfig['label']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
955
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
956 def add_final_data(self, data):
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
957 viz_data = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
958 if len(data['visibility']['default_on']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
959 viz_data['defaultTracks'] = ','.join(data['visibility']['default_on'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
960
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
961 if len(data['visibility']['always']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
962 viz_data['alwaysOnTracks'] = ','.join(data['visibility']['always'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
963
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
964 if len(data['visibility']['force']) > 0:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
965 viz_data['forceTracks'] = ','.join(data['visibility']['force'])
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
966
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
967 generalData = {}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
968 if data['general']['aboutDescription'] is not None:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
969 generalData['aboutThisBrowser'] = {'description': data['general']['aboutDescription'].strip()}
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
970
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
971 generalData['view'] = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
972 'trackPadding': data['general']['trackPadding']
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
973 }
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
974 generalData['shareLink'] = (data['general']['shareLink'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
975 generalData['show_tracklist'] = (data['general']['show_tracklist'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
976 generalData['show_nav'] = (data['general']['show_nav'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
977 generalData['show_overview'] = (data['general']['show_overview'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
978 generalData['show_menu'] = (data['general']['show_menu'] == 'true')
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
979 generalData['hideGenomeOptions'] = (data['general']['hideGenomeOptions'] == 'true')
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
980 generalData['plugins'] = data['plugins']
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
981
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
982 viz_data.update(generalData)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
983 self._add_json(viz_data)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
984
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
985 if 'GCContent' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
986 self._add_track_json({
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
987 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
988 "type": "GCContent/View/Track/GCContentXY",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
989 "label": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
990 "key": "GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
991 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
992 "bicolor_pivot": 0.5,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
993 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
994 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
995 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
996 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
997 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
998 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
999 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1000 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1001 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1002 }
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1003 # TODO: Expose params for everyone.
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1004 })
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1005 self._add_track_json({
27
61ce21e36cb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 25
diff changeset
1006 "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1007 "type": "GCContent/View/Track/GCContentXY",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1008 "label": "GC skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1009 "key": "GCSkew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1010 "urlTemplate": "seq/genome.fasta",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1011 "gcMode": "skew",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1012 "min_score": -1,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1013 "bicolor_pivot": 0,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1014 "category": "GC Content",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1015 "metadata": {
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1016 "tool_tool": '<a target="_blank" href="https://github.com/elsiklab/gccontent/commit/030180e75a19fad79478d43a67c566ec6">elsiklab/gccontent</a>',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1017 "tool_tool_version": "5c8b0582ecebf9edf684c76af8075fb3d30ec3fa",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1018 "dataset_edam_format": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1019 "dataset_size": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1020 "history_display_name": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1021 "history_user_email": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1022 "metadata_dbkey": "",
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1023 }
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1024 # TODO: Expose params for everyone.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1025 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1026
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1027 if 'ComboTrackSelector' in data['plugins_python']:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1028 with open(os.path.join(self.outdir, 'data', 'trackList.json'), 'r') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1029 trackListJson = json.load(handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1030 trackListJson.update({
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1031 "trackSelector": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1032 "renameFacets": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1033 "tool_tool": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1034 "tool_tool_id": "Tool ID",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1035 "tool_tool_version": "Tool Version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1036 "dataset_edam_format": "EDAM",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1037 "dataset_size": "Size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1038 "history_display_name": "History Name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1039 "history_user_email": "Owner",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1040 "metadata_dbkey": "Dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1041 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1042 "displayColumns": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1043 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1044 "tool_tool",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1045 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1046 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1047 "dataset_size",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1048 "history_display_name",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1049 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1050 "metadata_dbkey",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1051 ],
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1052 "type": "Faceted",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1053 "title": ["Galaxy Metadata"],
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1054 "icon": "https://galaxyproject.org/images/logos/galaxy-icon-square.png",
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1055 "escapeHTMLInData": False
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1056 },
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1057 "trackMetadata": {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1058 "indexFacets": [
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1059 "category",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1060 "key",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1061 "tool_tool_id",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1062 "tool_tool_version",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1063 "dataset_edam_format",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1064 "history_user_email",
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1065 "history_display_name"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1066 ]
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1067 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1068 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1069 with open(os.path.join(self.outdir, 'data', 'trackList2.json'), 'w') as handle:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1070 json.dump(trackListJson, handle)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1071
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1072 def clone_jbrowse(self, jbrowse_dir, destination):
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1073 """Clone a JBrowse directory into a destination directory.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1074 """
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1075 # JBrowse seems to have included some bad symlinks, cp ignores bad symlinks
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1076 # unlike copytree
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1077 cmd = ['cp', '-r', os.path.join(jbrowse_dir, '.'), destination]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1078 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1079 subprocess.check_call(cmd)
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1080 cmd = ['mkdir', '-p', os.path.join(destination, 'data', 'raw')]
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1081 log.debug(' '.join(cmd))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1082 subprocess.check_call(cmd)
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1083
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1084 # http://unix.stackexchange.com/a/38691/22785
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1085 # JBrowse releases come with some broken symlinks
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1086 cmd = ['find', destination, '-type', 'l', '-xtype', 'l']
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1087 log.debug(' '.join(cmd))
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1088 symlinks = subprocess.check_output(cmd)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1089 for i in symlinks:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1090 try:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1091 os.unlink(i)
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1092 except OSError:
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1093 pass
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1094
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1095
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1096 if __name__ == '__main__':
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1097 parser = argparse.ArgumentParser(description="", epilog="")
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
1098 parser.add_argument('xml', type=argparse.FileType('r'), help='Track Configuration')
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1099
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1100 parser.add_argument('--jbrowse', help='Folder containing a jbrowse release')
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1101 parser.add_argument('--outdir', help='Output directory', default='out')
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1102 parser.add_argument('--standalone', help='Standalone mode includes a copy of JBrowse', action='store_true')
25
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iuc
parents: 24
diff changeset
1103 parser.add_argument('--version', '-V', action='version', version="%(prog)s 0.8.0")
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1104 args = parser.parse_args()
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1105
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1106 tree = ET.parse(args.xml.name)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1107 root = tree.getroot()
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1108
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1109 # This should be done ASAP
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1110 GALAXY_INFRASTRUCTURE_URL = root.find('metadata/galaxyUrl').text
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1111 # Sometimes this comes as `localhost` without a protocol
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1112 if not GALAXY_INFRASTRUCTURE_URL.startswith('http'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1113 # so we'll prepend `http://` and hope for the best. Requests *should*
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1114 # be GET and not POST so it should redirect OK
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1115 GALAXY_INFRASTRUCTURE_URL = 'http://' + GALAXY_INFRASTRUCTURE_URL
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1116
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1117 jc = JbrowseConnector(
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1118 jbrowse=args.jbrowse,
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1119 outdir=args.outdir,
17
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iuc
parents: 16
diff changeset
1120 genomes=[
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1121 {
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1122 'path': os.path.realpath(x.attrib['path']),
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1123 'meta': metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1124 }
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1125 for x in root.findall('metadata/genomes/genome')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1126 ],
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1127 standalone=args.standalone,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1128 gencode=root.find('metadata/gencode').text
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1129 )
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1130
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1131 extra_data = {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1132 'visibility': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1133 'default_on': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1134 'default_off': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1135 'force': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1136 'always': [],
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1137 },
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1138 'general': {
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1139 'defaultLocation': root.find('metadata/general/defaultLocation').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1140 'trackPadding': int(root.find('metadata/general/trackPadding').text),
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1141 'shareLink': root.find('metadata/general/shareLink').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1142 'aboutDescription': root.find('metadata/general/aboutDescription').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1143 'show_tracklist': root.find('metadata/general/show_tracklist').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1144 'show_nav': root.find('metadata/general/show_nav').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1145 'show_overview': root.find('metadata/general/show_overview').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1146 'show_menu': root.find('metadata/general/show_menu').text,
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1147 'hideGenomeOptions': root.find('metadata/general/hideGenomeOptions').text,
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1148 },
25
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iuc
parents: 24
diff changeset
1149 'plugins': [],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1150 'plugins_python': [],
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1151 }
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1152
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1153 plugins = root.find('plugins').attrib
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1154 if plugins['GCContent'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1155 extra_data['plugins_python'].append('GCContent')
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1156 extra_data['plugins'].append({
24
fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf
iuc
parents: 22
diff changeset
1157 'location': 'https://cdn.jsdelivr.net/gh/elsiklab/gccontent@5c8b0582ecebf9edf684c76af8075fb3d30ec3fa/',
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1158 'name': 'GCContent'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1159 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1160
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1161 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1162 # if plugins['Bookmarks'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1163 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1164 # 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/bookmarks-jbrowse@5242694120274c86e1ccd5cb0e5e943e78f82393/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1165 # 'name': 'Bookmarks'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1166 # })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1167
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1168 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1169 if plugins['ComboTrackSelector'] == 'True':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1170 extra_data['plugins_python'].append('ComboTrackSelector')
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1171 # Not needed in 1.16.1: it's built in the conda package now, and this plugin doesn't need to be enabled anywhere
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1172 # extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1173 # 'location': 'https://cdn.jsdelivr.net/gh/Arabidopsis-Information-Portal/ComboTrackSelector@52403928d5ccbe2e3a86b0fa5eb8e61c0f2e2f57/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1174 # 'icon': 'https://galaxyproject.org/images/logos/galaxy-icon-square.png',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1175 # 'name': 'ComboTrackSelector'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1176 # })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1177
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1178 if plugins['theme'] == 'Minimalist':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1179 extra_data['plugins'].append({
24
fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf
iuc
parents: 22
diff changeset
1180 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-minimalist-theme@d698718442da306cf87f033c72ddb745f3077775/',
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1181 'name': 'MinimalistTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1182 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1183 elif plugins['theme'] == 'Dark':
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1184 extra_data['plugins'].append({
24
fa30df9b79c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 309588eae8df8baffaf49fc00fb0d28106109ddf
iuc
parents: 22
diff changeset
1185 'location': 'https://cdn.jsdelivr.net/gh/erasche/jbrowse-dark-theme@689eceb7e33bbc1b9b15518d45a5a79b2e5d0a26/',
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1186 'name': 'DarkTheme'
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1187 })
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1188
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1189 if plugins['BlastView'] == 'True':
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1190 extra_data['plugins_python'].append('BlastView')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1191 extra_data['plugins'].append({
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1192 'location': 'https://cdn.jsdelivr.net/gh/TAMU-CPT/blastview@97572a21b7f011c2b4d9a0b5af40e292d694cbef/',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1193 'name': 'BlastView'
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1194 })
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1195
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1196 for track in root.findall('tracks/track'):
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1197 track_conf = {}
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1198 track_conf['trackfiles'] = []
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1199
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1200 is_multi_bigwig = False
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1201 try:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1202 if track.find('options/wiggle/multibigwig') and (track.find('options/wiggle/multibigwig').text == 'True'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1203 is_multi_bigwig = True
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1204 multi_bigwig_paths = []
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1205 except KeyError:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1206 pass
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1207
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1208 trackfiles = track.findall('files/trackFile')
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1209 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1210 for x in track.findall('files/trackFile'):
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1211 if is_multi_bigwig:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1212 multi_bigwig_paths.append((x.attrib['label'], os.path.realpath(x.attrib['path'])))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1213 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1214 if trackfiles:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1215 metadata = metadata_from_node(x.find('metadata'))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1216
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1217 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1218 os.path.realpath(x.attrib['path']),
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1219 x.attrib['ext'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1220 x.attrib['label'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1221 metadata
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1222 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1223 else:
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1224 # For tracks without files (rest, sparql)
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1225 track_conf['trackfiles'].append((
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1226 '', # N/A, no path for rest or sparql
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1227 track.attrib['format'],
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1228 track.find('options/label').text,
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1229 {}
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1230 ))
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1231
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1232 if is_multi_bigwig:
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1233 metadata = metadata_from_node(x.find('metadata'))
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1234
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1235 track_conf['trackfiles'].append((
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1236 multi_bigwig_paths, # Passing an array of paths to represent as one track
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1237 'bigwig_multiple',
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1238 'MultiBigWig', # Giving an hardcoded name for now
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1239 {} # No metadata for multiple bigwig
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
1240 ))
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
1241
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1242 track_conf['category'] = track.attrib['cat']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1243 track_conf['format'] = track.attrib['format']
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1244 try:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1245 # Only pertains to gff3 + blastxml. TODO?
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1246 track_conf['style'] = {t.tag: t.text for t in track.find('options/style')}
25
1cfc579079a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents: 24
diff changeset
1247 except TypeError:
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1248 track_conf['style'] = {}
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1249 pass
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1250 track_conf['conf'] = etree_to_dict(track.find('options'))
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1251 keys = jc.process_annotations(track_conf)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1252
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1253 for key in keys:
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1254 extra_data['visibility'][track.attrib.get('visibility', 'default_off')].append(key)
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1255
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
1256 jc.add_final_data(extra_data)
20
558d652cd681 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75a0a1c7b26cac156f76e8266a0e2e3d81be7f02
iuc
parents: 17
diff changeset
1257 jc.generate_names()