Mercurial > repos > fubar > jbrowse2

annotate jbrowse2broken.py @ 58:0e592dcaeb7f draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author fubar
date Thu, 21 Mar 2024 09:06:52 +0000
parents 94264fe60478
children
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1 #!/usr/bin/env python
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2 # change to accumulating all configuration for config.json based on the default from the clone
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3 import argparse
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4 import binascii
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5 import datetime
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6 import json
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7 import logging
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8 import os
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9 import re
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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 urllib.request
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15 import xml.etree.ElementTree as ET
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16 from collections import defaultdict
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17
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18 logging.basicConfig(level=logging.INFO)
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19 log = logging.getLogger("jbrowse")
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20
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21 JB2VER = "v2.10.3"
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22 # version pinned for cloning
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23
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24 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
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25 GALAXY_INFRASTRUCTURE_URL = None
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26
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27 # version pinned for cloning
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28
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29 mapped_chars = {
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30 ">": "__gt__",
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31 "<": "__lt__",
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32 "'": "__sq__",
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33 '"': "__dq__",
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34 "[": "__ob__",
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35 "]": "__cb__",
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36 "{": "__oc__",
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37 "}": "__cc__",
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38 "@": "__at__",
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39 "#": "__pd__",
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40 "": "__cn__",
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41 }
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42
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43
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44 class ColorScaling(object):
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45
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46 COLOR_FUNCTION_TEMPLATE = """
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47 function(feature, variableName, glyphObject, track) {{
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48 var score = {score};
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49 {opacity}
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50 return 'rgba({red}, {green}, {blue}, ' + opacity + ')';
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51 }}
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52 """
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53
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54 COLOR_FUNCTION_TEMPLATE_QUAL = r"""
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55 function(feature, variableName, glyphObject, track) {{
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56 var search_up = function self(sf, attr){{
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57 if(sf.get(attr) !== undefined){{
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58 return sf.get(attr);
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59 }}
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60 if(sf.parent() === undefined) {{
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61 return;
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62 }}else{{
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63 return self(sf.parent(), attr);
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64 }}
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65 }};
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66
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67 var search_down = function self(sf, attr){{
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68 if(sf.get(attr) !== undefined){{
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69 return sf.get(attr);
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70 }}
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71 if(sf.children() === undefined) {{
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72 return;
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73 }}else{{
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74 var kids = sf.children();
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75 for(var child_idx in kids){{
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76 var x = self(kids[child_idx], attr);
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77 if(x !== undefined){{
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78 return x;
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79 }}
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80 }}
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81 return;
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82 }}
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83 }};
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84
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85 var color = ({user_spec_color} || search_up(feature, 'color') || search_down(feature, 'color') || {auto_gen_color});
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86 var score = (search_up(feature, 'score') || search_down(feature, 'score'));
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87 {opacity}
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88 if(score === undefined){{ opacity = 1; }}
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89 var result = /^#?([a-f\d]{{2}})([a-f\d]{{2}})([a-f\d]{{2}})$/i.exec(color);
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90 var red = parseInt(result[1], 16);
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91 var green = parseInt(result[2], 16);
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
92 var blue = parseInt(result[3], 16);
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
93 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
94 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')';
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
95 }}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
96 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
97
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
98 OPACITY_MATH = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
99 "linear": """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
100 var opacity = (score - ({min})) / (({max}) - ({min}));
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
101 """,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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102 "logarithmic": """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
103 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
104 """,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
105 "blast": """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
106 var opacity = 0;
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diff changeset
107 if(score == 0.0) {{
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
108 opacity = 1;
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diff changeset
109 }} else {{
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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110 opacity = (20 - Math.log10(score)) / 180;
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
111 }}
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diff changeset
112 """,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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113 }
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114
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115 BREWER_COLOUR_IDX = 0
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116 BREWER_COLOUR_SCHEMES = [
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117 (166, 206, 227),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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118 (31, 120, 180),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
119 (178, 223, 138),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
120 (51, 160, 44),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
121 (251, 154, 153),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
122 (227, 26, 28),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
123 (253, 191, 111),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
124 (255, 127, 0),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
125 (202, 178, 214),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
126 (106, 61, 154),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
127 (255, 255, 153),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
128 (177, 89, 40),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
129 (228, 26, 28),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
130 (55, 126, 184),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
131 (77, 175, 74),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
132 (152, 78, 163),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
133 (255, 127, 0),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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134 ]
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135
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136 BREWER_DIVERGING_PALLETES = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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137 "BrBg": ("#543005", "#003c30"),
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138 "PiYg": ("#8e0152", "#276419"),
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139 "PRGn": ("#40004b", "#00441b"),
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140 "PuOr": ("#7f3b08", "#2d004b"),
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141 "RdBu": ("#67001f", "#053061"),
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142 "RdGy": ("#67001f", "#1a1a1a"),
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143 "RdYlBu": ("#a50026", "#313695"),
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144 "RdYlGn": ("#a50026", "#006837"),
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145 "Spectral": ("#9e0142", "#5e4fa2"),
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146 }
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147
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148 def __init__(self):
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149 self.brewer_colour_idx = 0
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diff changeset
150
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151 def rgb_from_hex(self, hexstr):
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152 # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back
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153 return struct.unpack("BBB", binascii.unhexlify(hexstr))
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154
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155 def min_max_gff(self, gff_file):
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156 min_val = None
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157 max_val = None
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158 with open(gff_file, "r") as handle:
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diff changeset
159 for line in handle:
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diff changeset
160 try:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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161 value = float(line.split("\t")[5])
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162 min_val = min(value, (min_val or value))
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163 max_val = max(value, (max_val or value))
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diff changeset
164
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165 if value < min_val:
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diff changeset
166 min_val = value
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diff changeset
167
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diff changeset
168 if value > max_val:
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diff changeset
169 max_val = value
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diff changeset
170 except Exception:
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diff changeset
171 pass
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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172 return min_val, max_val
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173
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174 def hex_from_rgb(self, r, g, b):
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175 return "#%02x%02x%02x" % (r, g, b)
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176
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177 def _get_colours(self):
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178 r, g, b = self.BREWER_COLOUR_SCHEMES[
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diff changeset
179 self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)
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180 ]
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diff changeset
181 self.brewer_colour_idx += 1
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182 return r, g, b
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183
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184 def parse_menus(self, track):
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185 trackConfig = {"menuTemplate": [{}, {}, {}, {}]}
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186
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187 if "menu" in track["menus"]:
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188 menu_list = [track["menus"]["menu"]]
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189 if isinstance(track["menus"]["menu"], list):
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190 menu_list = track["menus"]["menu"]
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191
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192 for m in menu_list:
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193 tpl = {
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194 "action": m["action"],
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195 "label": m.get("label", "{name}"),
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196 "iconClass": m.get("iconClass", "dijitIconBookmark"),
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197 }
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198 if "url" in m:
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199 tpl["url"] = m["url"]
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200 if "content" in m:
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201 tpl["content"] = m["content"]
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202 if "title" in m:
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203 tpl["title"] = m["title"]
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204
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205 trackConfig["menuTemplate"].append(tpl)
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206
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207 return trackConfig
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208
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209 def parse_colours(self, track, trackFormat, gff3=None):
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210 # Wiggle tracks have a bicolor pallete
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211 trackConfig = {"style": {}}
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212 if trackFormat == "wiggle":
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213
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214 trackConfig["style"]["pos_color"] = track["wiggle"]["color_pos"]
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215 trackConfig["style"]["neg_color"] = track["wiggle"]["color_neg"]
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216
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217 if trackConfig["style"]["pos_color"] == "__auto__":
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218 trackConfig["style"]["neg_color"] = self.hex_from_rgb(
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219 *self._get_colours()
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220 )
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221 trackConfig["style"]["pos_color"] = self.hex_from_rgb(
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222 *self._get_colours()
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223 )
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224
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225 # Wiggle tracks can change colour at a specified place
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226 bc_pivot = track["wiggle"]["bicolor_pivot"]
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227 if bc_pivot not in ("mean", "zero"):
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228 # The values are either one of those two strings
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229 # or a number
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230 bc_pivot = float(bc_pivot)
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231 trackConfig["bicolor_pivot"] = bc_pivot
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232 elif "scaling" in track:
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233 if track["scaling"]["method"] == "ignore":
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234 if track["scaling"]["scheme"]["color"] != "__auto__":
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235 trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"]
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236 else:
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237 trackConfig["style"]["color"] = self.hex_from_rgb(
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238 *self._get_colours()
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239 )
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240 else:
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241 # Scored method
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242 algo = track["scaling"]["algo"]
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243 # linear, logarithmic, blast
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244 scales = track["scaling"]["scales"]
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245 # type __auto__, manual (min, max)
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246 scheme = track["scaling"]["scheme"]
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247 # scheme -> (type (opacity), color)
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248 # ==================================
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249 # GENE CALLS OR BLAST
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250 # ==================================
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251 if trackFormat == "blast":
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252 red, green, blue = self._get_colours()
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253 color_function = self.COLOR_FUNCTION_TEMPLATE.format(
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254 **{
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255 "score": "feature._parent.get('score')",
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256 "opacity": self.OPACITY_MATH["blast"],
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257 "red": red,
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258 "green": green,
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259 "blue": blue,
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260 }
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261 )
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262 trackConfig["style"]["color"] = color_function.replace("\n", "")
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263 elif trackFormat == "gene_calls":
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264 # Default values, based on GFF3 spec
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265 min_val = 0
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266 max_val = 1000
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267 # Get min/max and build a scoring function since JBrowse doesn't
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268 if scales["type"] == "automatic" or scales["type"] == "__auto__":
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269 min_val, max_val = self.min_max_gff(gff3)
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270 else:
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271 min_val = scales.get("min", 0)
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272 max_val = scales.get("max", 1000)
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273
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274 if scheme["color"] == "__auto__":
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275 user_color = "undefined"
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276 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
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277 elif scheme["color"].startswith("#"):
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278 user_color = "'%s'" % self.hex_from_rgb(
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279 *self.rgb_from_hex(scheme["color"][1:])
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280 )
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diff changeset
281 auto_color = "undefined"
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diff changeset
282 else:
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283 user_color = "undefined"
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284 auto_color = "'%s'" % self.hex_from_rgb(*self._get_colours())
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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285
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286 color_function = self.COLOR_FUNCTION_TEMPLATE_QUAL.format(
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287 **{
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288 "opacity": self.OPACITY_MATH[algo].format(
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289 **{"max": max_val, "min": min_val}
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290 ),
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291 "user_spec_color": user_color,
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292 "auto_gen_color": auto_color,
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293 }
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294 )
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295
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296 trackConfig["style"]["color"] = color_function.replace("\n", "")
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297 return trackConfig
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298
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299
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300 def etree_to_dict(t):
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301 if t is None:
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302 return {}
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303
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304 d = {t.tag: {} if t.attrib else None}
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305 children = list(t)
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306 if children:
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307 dd = defaultdict(list)
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308 for dc in map(etree_to_dict, children):
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309 for k, v in dc.items():
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310 dd[k].append(v)
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311 d = {t.tag: {k: v[0] if len(v) == 1 else v for k, v in dd.items()}}
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312 if t.attrib:
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313 d[t.tag].update(("@" + k, v) for k, v in t.attrib.items())
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314 if t.text:
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parents:
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315 text = t.text.strip()
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diff changeset
316 if children or t.attrib:
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diff changeset
317 if text:
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318 d[t.tag]["#text"] = text
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diff changeset
319 else:
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320 d[t.tag] = text
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diff changeset
321 return d
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diff changeset
322
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diff changeset
323
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324 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__))
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diff changeset
325
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diff changeset
326
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327 def metadata_from_node(node):
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diff changeset
328 metadata = {}
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parents:
diff changeset
329 try:
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330 if len(node.findall("dataset")) != 1:
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diff changeset
331 # exit early
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parents:
diff changeset
332 return metadata
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diff changeset
333 except Exception:
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diff changeset
334 return {}
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parents:
diff changeset
335
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
336 for (key, value) in node.findall("dataset")[0].attrib.items():
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diff changeset
337 metadata["dataset_%s" % key] = value
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diff changeset
338
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diff changeset
339 if node.findall("history"):
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diff changeset
340 for (key, value) in node.findall("history")[0].attrib.items():
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
341 metadata["history_%s" % key] = value
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diff changeset
342
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
343 if node.findall("metadata"):
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diff changeset
344 for (key, value) in node.findall("metadata")[0].attrib.items():
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diff changeset
345 metadata["metadata_%s" % key] = value
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diff changeset
346 # Additional Mappings applied:
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diff changeset
347 metadata[
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
348 "dataset_edam_format"
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349 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
350 metadata["dataset_edam_format"], metadata["dataset_file_ext"]
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diff changeset
351 )
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parents:
diff changeset
352 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
353 metadata["history_user_email"]
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diff changeset
354 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
355 metadata["hist_name"] = metadata["history_display_name"]
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fubar
parents:
diff changeset
356 metadata[
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
357 "history_display_name"
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parents:
diff changeset
358 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
359 galaxy=GALAXY_INFRASTRUCTURE_URL,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
360 encoded_hist_id=metadata["history_id"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
361 hist_name=metadata["history_display_name"],
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diff changeset
362 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
363 if node.findall("tool"):
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diff changeset
364 for (key, value) in node.findall("tool")[0].attrib.items():
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diff changeset
365 metadata["tool_%s" % key] = value
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diff changeset
366 metadata[
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff changeset
367 "tool_tool"
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368 ] = '<a target="_blank" href="{galaxy}/datasets/{encoded_id}/show_params">{tool_id}{tool_version}</a>'.format(
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diff changeset
369 galaxy=GALAXY_INFRASTRUCTURE_URL,
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370 encoded_id=metadata.get("dataset_id", ""),
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diff changeset
371 tool_id=metadata.get("tool_tool_id", ""),
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diff changeset
372 tool_version=metadata.get("tool_tool_version", ""),
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diff changeset
373 )
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diff changeset
374 return metadata
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diff changeset
375
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diff changeset
376
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parents:
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377 class JbrowseConnector(object):
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378 def __init__(self, outdir, jbrowse2path, genomes):
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379 self.giURL = GALAXY_INFRASTRUCTURE_URL
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380 self.outdir = outdir
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381 self.jbrowse2path = jbrowse2path
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382 os.makedirs(self.outdir, exist_ok=True)
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383 self.genome_paths = genomes
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384 self.genome_name = None
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385 self.genome_names = []
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386 self.trackIdlist = []
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387 self.tracksToAdd = []
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388 self.config_json = {}
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389 self.config_json_file = os.path.join(outdir, "config.json")
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parents:
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390 self.clone_jbrowse()
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diff changeset
391
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392 def subprocess_check_call(self, command, output=None):
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393 if output:
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parents:
diff changeset
394 log.debug("cd %s && %s > %s", self.outdir, " ".join(command), output)
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395 subprocess.check_call(command, cwd=self.outdir, stdout=output)
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diff changeset
396 else:
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diff changeset
397 log.debug("cd %s && %s", self.outdir, " ".join(command))
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diff changeset
398 subprocess.check_call(command, cwd=self.outdir)
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diff changeset
399
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400 def subprocess_popen(self, command):
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diff changeset
401 log.debug(command)
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diff changeset
402 p = subprocess.Popen(
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parents:
diff changeset
403 command,
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diff changeset
404 cwd=self.outdir,
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diff changeset
405 shell=True,
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parents:
diff changeset
406 stdin=subprocess.PIPE,
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diff changeset
407 stdout=subprocess.PIPE,
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parents:
diff changeset
408 stderr=subprocess.PIPE,
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diff changeset
409 )
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parents:
diff changeset
410 output, err = p.communicate()
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parents:
diff changeset
411 retcode = p.returncode
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parents:
diff changeset
412 if retcode != 0:
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diff changeset
413 log.error(command)
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diff changeset
414 log.error(output)
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parents:
diff changeset
415 log.error(err)
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parents:
diff changeset
416 raise RuntimeError("Command failed with exit code %s" % (retcode))
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diff changeset
417
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parents:
diff changeset
418 def _prepare_track_style(self, trackDict):
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diff changeset
419 style_data = {
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parents:
diff changeset
420 "type": "LinearBasicDisplay",
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parents:
diff changeset
421 "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"],
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diff changeset
422 }
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diff changeset
423
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parents:
diff changeset
424 if trackDict.get("displays", None): # use first if multiple like bed
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parents:
diff changeset
425 style_data["type"] = trackDict["displays"][0]["type"]
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diff changeset
426 style_data["displayId"] = trackDict["displays"][0]["displayId"]
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parents:
diff changeset
427 return {
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parents:
diff changeset
428 "displays": [
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diff changeset
429 style_data,
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parents:
diff changeset
430 ]
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parents:
diff changeset
431 }
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parents:
diff changeset
432
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parents:
diff changeset
433 def subprocess_check_output(self, command):
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parents:
diff changeset
434 log.debug(" ".join(command))
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diff changeset
435 return subprocess.check_output(command, cwd=self.outdir)
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parents:
diff changeset
436
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parents:
diff changeset
437 def symlink_or_copy(self, src, dest):
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parents:
diff changeset
438 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
439 os.environ["GALAXY_JBROWSE_SYMLINKS"]
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parents:
diff changeset
440 ):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
441 cmd = ["ln", "-s", src, dest]
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diff changeset
442 else:
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parents:
diff changeset
443 cmd = ["cp", src, dest]
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parents:
diff changeset
444
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
445 return self.subprocess_check_call(cmd)
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parents:
diff changeset
446
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parents:
diff changeset
447 def process_genomes(self):
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parents:
diff changeset
448 assemblies = []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
449 useuri = False
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parents:
diff changeset
450 for i, genome_node in enumerate(self.genome_paths):
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parents:
diff changeset
451 if genome_node["useuri"].strip().lower() == "yes":
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parents:
diff changeset
452 useuri = True
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diff changeset
453 genome_name = genome_node["meta"]["dataset_dname"].strip()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
454 if len(genome_name.split()) > 1:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
455 genome_name = genome_name.split()[0]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
456 # spaces and cruft break scripts when substituted
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
457 if genome_name not in self.genome_names:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
458 # ignore dupes - can have multiple pafs with same references?
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
459 fapath = genome_node["path"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
460 if not useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
461 fapath = os.path.realpath(fapath)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
462 assem = self.make_assembly(fapath, genome_name, useuri)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
463 assemblies.append(assem)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
464 self.genome_names.append(genome_name)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
465 if self.genome_name is None:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
466 self.genome_name = (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
467 genome_name # first one for all tracks - other than paf
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
468 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
469 self.genome_sequence_adapter = assem["sequence"]["adapter"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
470 self.genome_firstcontig = None
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
471 if not useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
472 fl = open(fapath, "r").readline()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
473 fls = fl.strip().split(">")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
474 if len(fls) > 1:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
475 fl = fls[1]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
476 if len(fl.split()) > 1:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
477 self.genome_firstcontig = fl.split()[0].strip()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
478 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
479 self.genome_firstcontig = fl
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
480 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
481 fl = urllib.request.urlopen(fapath + ".fai").readline()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
482 if fl: # is first row of the text fai so the first contig name
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
483 self.genome_firstcontig = (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
484 fl.decode("utf8").strip().split()[0]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
485 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
486 if self.config_json.get("assemblies", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
487 self.config_json["assemblies"] += assemblies
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
488 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
489 self.config_json["assemblies"] = assemblies
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
490
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
491 def make_assembly(self, fapath, gname, useuri):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
492 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
493 faname = fapath
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
494 adapter = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
495 "type": "BgzipFastaAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
496 "fastaLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
497 "uri": faname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
498 "locationType": "UriLocation",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
499 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
500 "faiLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
501 "uri": faname + ".fai",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
502 "locationType": "UriLocation",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
503 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
504 "gziLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
505 "uri": faname + ".gzi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
506 "locationType": "UriLocation",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
507 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
508 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
509 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
510 faname = gname + ".fa.gz"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
511 fadest = os.path.realpath(os.path.join(self.outdir, faname))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
512 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
513 fapath,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
514 fadest,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
515 fadest,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
516 fadest,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
517 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
518 self.subprocess_popen(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
519
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
520 adapter = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
521 "type": "BgzipFastaAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
522 "fastaLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
523 "uri": faname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
524 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
525 "faiLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
526 "uri": faname + ".fai",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
527 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
528 "gziLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
529 "uri": faname + ".gzi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
530 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
531 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
532
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
533 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
534 "name": gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
535 "sequence": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
536 "type": "ReferenceSequenceTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
537 "trackId": gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
538 "adapter": adapter,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
539 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
540 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
541 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
542 "type": "LinearReferenceSequenceDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
543 "displayId": "%s-LinearReferenceSequenceDisplay" % gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
544 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
545 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
546 "type": "LinearGCContentDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
547 "displayId": "%s-LinearGCContentDisplay" % gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
548 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
549 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
550 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
551 return trackDict
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
552
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
553 def add_default_view(self):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
554 cmd = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
555 "jbrowse",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
556 "set-default-session",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
557 "-s",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
558 self.config_json_file,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
559 "-t",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
560 ",".join(self.trackIdlist),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
561 "-n",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
562 "JBrowse2 in Galaxy",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
563 "--target",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
564 self.config_json_file,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
565 "-v",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
566 " LinearGenomeView",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
567 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
568 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
569
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
570 def write_config(self):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
571 with open(self.config_json_file, "w") as fp:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
572 json.dump(self.config_json, fp, indent=2)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
573
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
574 def text_index(self):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
575 # Index tracks
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
576 args = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
577 "jbrowse",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
578 "text-index",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
579 "--target",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
580 os.path.join(self.outdir, "data"),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
581 "--assemblies",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
582 self.genome_name,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
583 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
584
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
585 tracks = ",".join(self.trackIdlist)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
586 if tracks:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
587 args += ["--tracks", tracks]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
588
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
589 self.subprocess_check_call(args)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
590
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
591 def add_hic(self, data, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
592 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
593 HiC adapter.
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
594 https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
595 for testing locally, these work:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
596 HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
597 using hg19 reference track as a
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
598 'BgzipFastaAdapter'
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
599 fastaLocation:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
600 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz',
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
601 faiLocation:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
602 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai',
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
603 gziLocation:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
604 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi',
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
605 Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
606 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
607 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
608 # can be served - if public.
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
609 # dsId = trackData["metadata"]["dataset_id"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
610 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
611 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
612 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
613 uri = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
614 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
615 uri = trackData["hic_url"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
616 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
617 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
618 "type": "HicTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
619 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
620 "name": uri,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
621 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
622 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
623 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
624 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
625 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
626 "type": "HicAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
627 "hicLocation": uri,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
628 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
629 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
630 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
631 "type": "LinearHicDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
632 "displayId": "%s-LinearHicDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
633 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
634 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
635 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
636 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
637 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
638 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
639 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
640
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
641 def add_maf(self, data, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
642 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
643 from https://github.com/cmdcolin/maf2bed
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
644 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
645 e.g. hg38.chr1 in the sequence identifiers.
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
646 need the reference id - eg hg18, for maf2bed.pl as the first parameter
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
647 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
648 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
649 mafPlugin = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
650 "plugins": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
651 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
652 "name": "MafViewer",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
653 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
654 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
655 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
656 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
657 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
658 fname = "%s.bed" % tId
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
659 dest = "%s/%s" % (self.outdir, fname)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
660 gname = self.genome_name
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
661 cmd = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
662 "bash",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
663 os.path.join(INSTALLED_TO, "convertMAF.sh"),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
664 data,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
665 gname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
666 INSTALLED_TO,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
667 dest,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
668 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
669 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
670 # Construct samples list
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
671 # We could get this from galaxy metadata, not sure how easily.
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
672 ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
673 output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
674 ps.wait()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
675 outp = output.decode("ascii")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
676 soutp = outp.split("\n")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
677 samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
678 samples = [x.split(".")[0] for x in samp]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
679 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
680 "type": "MafTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
681 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
682 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
683 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
684 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
685 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
686 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
687 "type": "MafTabixAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
688 "samples": samples,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
689 "bedGzLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
690 "uri": fname + ".sorted.bed.gz",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
691 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
692 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
693 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
694 "uri": fname + ".sorted.bed.gz.tbi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
695 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
696 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
697 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
698 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
699 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
700 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
701 "type": "LinearBasicDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
702 "displayId": "%s-LinearBasicDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
703 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
704 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
705 "type": "LinearArcDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
706 "displayId": "%s-LinearArcDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
707 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
708 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
709 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
710 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
711 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
712 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
713 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
714 if self.config_json.get("plugins", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
715 self.config_json["plugins"].append(mafPlugin[0])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
716 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
717 self.config_json.update(mafPlugin)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
718
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
719 def _blastxml_to_gff3(self, xml, min_gap=10):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
720 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
721 cmd = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
722 "python",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
723 os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
724 "--trim",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
725 "--trim_end",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
726 "--include_seq",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
727 "--min_gap",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
728 str(min_gap),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
729 xml,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
730 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
731 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
732 gff3_unrebased.close()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
733 return gff3_unrebased.name
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
734
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
735 def add_blastxml(self, data, trackData, blastOpts, **kwargs):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
736 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
737
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
738 if "parent" in blastOpts and blastOpts["parent"] != "None":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
739 gff3_rebased = tempfile.NamedTemporaryFile(delete=False)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
740 cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
741 if blastOpts.get("protein", "false") == "true":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
742 cmd.append("--protein2dna")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
743 cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
744 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
745 gff3_rebased.close()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
746
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
747 # Replace original gff3 file
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
748 shutil.copy(gff3_rebased.name, gff3)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
749 os.unlink(gff3_rebased.name)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
750 url = "%s.gff3" % trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
751 dest = "%s/%s" % (self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
752 self._sort_gff(gff3, dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
753 url = url + ".gz"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
754 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
755 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
756 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
757 "type": "FeatureTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
758 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
759 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
760 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
761 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
762 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
763 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
764 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
765 "type": "Gff3TabixAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
766 "gffGzLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
767 "uri": url,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
768 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
769 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
770 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
771 "uri": url + ".tbi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
772 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
773 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
774 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
775 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
776 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
777 "type": "LinearBasicDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
778 "displayId": "%s-LinearBasicDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
779 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
780 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
781 "type": "LinearArcDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
782 "displayId": "%s-LinearArcDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
783 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
784 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
785 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
786 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
787 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
788 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
789 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
790 os.unlink(gff3)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
791
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
792 def add_bigwig(self, data, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
793 """ "type": "LinearWiggleDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
794 "configuration": {},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
795 "selectedRendering": "",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
796 "resolution": 1,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
797 "posColor": "rgb(228, 26, 28)",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
798 "negColor": "rgb(255, 255, 51)",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
799 "constraints": {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
800 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
801 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
802 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
803 url = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
804 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
805 url = "%s.bigwig" % trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
806 # slashes in names cause path trouble
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
807 dest = os.path.join(self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
808 cmd = ["cp", data, dest]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
809 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
810 bwloc = {"uri": url}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
811 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
812 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
813 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
814 "type": "QuantitativeTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
815 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
816 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
817 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
818 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
819 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
820 "assemblyNames": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
821 self.genome_name,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
822 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
823 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
824 "type": "BigWigAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
825 "bigWigLocation": bwloc,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
826 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
827 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
828 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
829 "type": "LinearWiggleDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
830 "displayId": "%s-LinearWiggleDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
831 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
832 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
833 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
834 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
835 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
836 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
837 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
838
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
839 def add_bam(self, data, trackData, bam_index=None, **kwargs):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
840 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
841 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
842 bindex = bam_index
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
843 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
844 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
845 url = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
846 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
847 fname = "%s.bam" % trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
848 dest = "%s/%s" % (self.outdir, fname)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
849 url = fname
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
850 bindex = fname + ".bai"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
851 self.subprocess_check_call(["cp", data, dest])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
852 if bam_index is not None and os.path.exists(bam_index):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
853 if not os.path.exists(bindex):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
854 # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
855 self.subprocess_check_call(["cp", bam_index, bindex])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
856 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
857 # Can happen in exotic condition
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
858 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
859 # => no index generated by galaxy, but there might be one next to the symlink target
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
860 # this trick allows to skip the bam sorting made by galaxy if already done outside
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
861 if os.path.exists(os.path.realpath(data) + ".bai"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
862 self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
863 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
864 log.warn("Could not find a bam index (.bai file) for %s", data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
865 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
866 "type": "AlignmentsTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
867 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
868 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
869 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
870 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
871 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
872 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
873 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
874 "type": "BamAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
875 "bamLocation": {"uri": url},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
876 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
877 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
878 "uri": bindex,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
879 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
880 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
881 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
882 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
883 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
884 "type": "LinearAlignmentsDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
885 "displayId": "%s-LinearAlignmentsDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
886 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
887 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
888 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
889 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
890 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
891 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
892 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
893
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
894 def add_cram(self, data, trackData, cram_index=None, **kwargs):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
895 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
896 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
897 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
898 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
899 url = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
900 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
901 fname = "%s.cram" % trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
902 dest = "%s/%s" % (self.outdir, fname)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
903 url = fname
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
904 self.subprocess_check_call(["cp", data, dest])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
905 if cram_index is not None and os.path.exists(cram_index):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
906 if not os.path.exists(dest + ".crai"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
907 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
908 self.subprocess_check_call(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
909 ["cp", os.path.realpath(cram_index), dest + ".crai"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
910 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
911 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
912 cpath = os.path.realpath(dest) + ".crai"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
913 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
914 logging.debug("executing cmd %s" % " ".join(cmd))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
915 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
916 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
917 "type": "AlignmentsTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
918 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
919 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
920 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
921 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
922 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
923 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
924 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
925 "type": "CramAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
926 "cramLocation": {"uri": url},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
927 "craiLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
928 "uri": url + ".crai",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
929 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
930 "sequenceAdapter": self.genome_sequence_adapter,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
931 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
932 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
933 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
934 "type": "LinearAlignmentsDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
935 "displayId": "%s-LinearAlignmentsDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
936 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
937 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
938 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
939 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
940 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
941 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
942 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
943
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
944 def add_vcf(self, data, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
945 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
946 # url = "%s/api/datasets/%s/display" % (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
947 # self.giURL,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
948 # trackData["metadata"]["dataset_id"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
949 # )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
950 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
951 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
952 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
953 url = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
954 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
955 url = "%s.vcf.gz" % tId
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
956 dest = "%s/%s" % (self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
957 cmd = "bgzip -c %s > %s" % (data, dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
958 self.subprocess_popen(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
959 cmd = ["tabix", "-f", "-p", "vcf", dest]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
960 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
961 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
962 "type": "VariantTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
963 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
964 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
965 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
966 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
967 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
968 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
969 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
970 "type": "VcfTabixAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
971 "vcfGzLocation": {"uri": url},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
972 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
973 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
974 "uri": url + ".tbi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
975 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
976 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
977 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
978 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
979 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
980 "type": "LinearVariantDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
981 "displayId": "%s-LinearVariantDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
982 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
983 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
984 "type": "ChordVariantDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
985 "displayId": "%s-ChordVariantDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
986 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
987 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
988 "type": "LinearPairedArcDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
989 "displayId": "%s-LinearPairedArcDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
990 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
991 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
992 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
993 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
994 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
995 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
996 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
997
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
998 def _sort_gff(self, data, dest):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
999 # Only index if not already done
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1000 if not os.path.exists(dest):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1001 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1002 data,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1003 dest,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1004 ) # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1005 self.subprocess_popen(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1006 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1007
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1008 def _sort_bed(self, data, dest):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1009 # Only index if not already done
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1010 if not os.path.exists(dest):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1011 cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1012 self.subprocess_popen(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1013 cmd = ["tabix", "-f", "-p", "bed", dest]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1014 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1015
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1016 def add_gff(self, data, ext, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1017 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1018 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1019 url = trackData["path"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1020 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1021 url = "%s.%s.gz" % (trackData["label"], ext)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1022 dest = "%s/%s" % (self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1023 self._sort_gff(data, dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1024 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1025 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1026 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1027 "type": "FeatureTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1028 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1029 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1030 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1031 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1032 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1033 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1034 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1035 "type": "Gff3TabixAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1036 "gffGzLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1037 "uri": url,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1038 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1039 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1040 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1041 "uri": url + ".tbi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1042 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1043 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1044 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1045 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1046 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1047 "type": "LinearBasicDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1048 "displayId": "%s-LinearBasicDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1049 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1050 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1051 "type": "LinearArcDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1052 "displayId": "%s-LinearArcDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1053 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1054 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1055 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1056 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1057 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1058 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1059 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1060
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1061 def add_bed(self, data, ext, trackData):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1062 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1063 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1064 useuri = trackData["useuri"].lower() == "yes"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1065 if useuri:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1066 url = data
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1067 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1068 url = "%s.%s.gz" % (trackData["label"], ext)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1069 dest = "%s/%s" % (self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1070 self._sort_bed(data, dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1071 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1072 "type": "FeatureTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1073 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1074 "name": trackData["name"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1075 "assemblyNames": [self.genome_name],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1076 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1077 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1078 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1079 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1080 "type": "BedTabixAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1081 "bedGzLocation": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1082 "uri": url,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1083 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1084 "index": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1085 "location": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1086 "uri": url + ".tbi",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1087 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1088 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1089 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1090 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1091 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1092 "type": "LinearBasicDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1093 "displayId": "%s-LinearBasicDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1094 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1095 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1096 "type": "LinearPileupDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1097 "displayId": "%s-LinearPileupDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1098 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1099 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1100 "type": "LinearArcDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1101 "displayId": "%s-LinearArcDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1102 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1103 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1104 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1105 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1106 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1107 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1108 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1109
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1110 def add_paf(self, data, trackData, pafOpts, **kwargs):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1111 tname = trackData["name"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1112 tId = trackData["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1113 categ = trackData["category"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1114 pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1115 pgpaths = [x.strip() for x in pafOpts["genome"].split(",")]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1116 passnames = [self.genome_name] # always first
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1117 for i, gname in enumerate(pgnames):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1118 if len(gname.split()) > 1:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1119 gname = gname.split()[0]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1120 passnames.append(gname)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1121 # trouble from spacey names in command lines avoidance
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1122 if gname not in self.genome_names:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1123 # ignore if already there - eg for duplicates among pafs.
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1124 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1125 "https://"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1126 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1127 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1128 self.genome_names.append(gname)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1129 if self.config_json.get("assemblies", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1130 self.config_json["assemblies"].append(asstrack)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1131 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1132 self.config_json["assemblies"] = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1133 asstrack,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1134 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1135 url = "%s.paf" % (trackData["label"])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1136 dest = "%s/%s" % (self.outdir, url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1137 self.symlink_or_copy(os.path.realpath(data), dest)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1138 trackDict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1139 "type": "SyntenyTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1140 "trackId": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1141 "assemblyNames": passnames,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1142 "category": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1143 categ,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1144 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1145 "name": tname,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1146 "adapter": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1147 "type": "PAFAdapter",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1148 "pafLocation": {"uri": url},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1149 "assemblyNames": passnames,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1150 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1151 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1152 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1153 "type": "LinearSyntenyDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1154 "displayId": "%s-LinearSyntenyDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1155 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1156 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1157 "type": "DotPlotDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1158 "displayId": "%s-DotPlotDisplay" % tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1159 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1160 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1161 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1162 style_json = self._prepare_track_style(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1163 trackDict["style"] = style_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1164 self.tracksToAdd.append(trackDict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1165 self.trackIdlist.append(tId)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1166
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1167 def process_annotations(self, track):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1168 category = track["category"].replace("__pd__date__pd__", TODAY)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1169 for i, (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1170 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1171 dataset_ext,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1172 useuri,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1173 track_human_label,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1174 extra_metadata,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1175 ) in enumerate(track["trackfiles"]):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1176 if not dataset_path.strip().startswith("http"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1177 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1178 for key, value in mapped_chars.items():
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1179 track_human_label = track_human_label.replace(value, key)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1180 track_human_label = track_human_label.replace(" ", "_")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1181 outputTrackConfig = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1182 "category": category,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1183 "style": track["style"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1184 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1185
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1186 outputTrackConfig["label"] = "%s_%i_%s" % (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1187 dataset_ext,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1188 i,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1189 track_human_label,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1190 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1191 outputTrackConfig["useuri"] = useuri
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1192 outputTrackConfig["path"] = dataset_path
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1193 outputTrackConfig["ext"] = dataset_ext
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1194 outputTrackConfig["key"] = track_human_label
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1195
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1196 outputTrackConfig["trackset"] = track.get("trackset", {})
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1197 outputTrackConfig["metadata"] = extra_metadata
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1198 outputTrackConfig["name"] = track_human_label
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1199
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1200 if dataset_ext in ("gff", "gff3"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1201 self.add_gff(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1202 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1203 dataset_ext,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1204 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1205 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1206 elif dataset_ext in ("hic", "juicebox_hic"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1207 self.add_hic(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1208 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1209 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1210 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1211 elif dataset_ext in ("cool", "mcool", "scool"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1212 hic_url = "%s_%d.juicebox_hic" % (track_human_label, i)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1213 hic_path = os.path.join(self.outdir, hic_url)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1214 self.subprocess_check_call(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1215 [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1216 "hictk",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1217 "convert",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1218 "-f",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1219 "--output-fmt",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1220 "hic",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1221 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1222 hic_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1223 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1224 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1225 outputTrackConfig["hic_url"] = hic_url
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1226 self.add_hic(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1227 hic_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1228 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1229 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1230 elif dataset_ext in ("bed",):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1231 self.add_bed(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1232 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1233 dataset_ext,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1234 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1235 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1236 elif dataset_ext in ("maf",):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1237 self.add_maf(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1238 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1239 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1240 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1241 elif dataset_ext == "bigwig":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1242 self.add_bigwig(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1243 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1244 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1245 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1246 elif dataset_ext == "bam":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1247 real_indexes = track["conf"]["options"]["bam"]["bam_index"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1248 self.add_bam(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1249 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1250 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1251 bam_index=real_indexes,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1252 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1253 elif dataset_ext == "cram":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1254 real_indexes = track["conf"]["options"]["cram"]["cram_index"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1255 self.add_cram(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1256 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1257 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1258 cram_index=real_indexes,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1259 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1260 elif dataset_ext == "blastxml":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1261 self.add_blastxml(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1262 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1263 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1264 track["conf"]["options"]["blast"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1265 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1266 elif dataset_ext == "vcf":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1267 self.add_vcf(dataset_path, outputTrackConfig)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1268 elif dataset_ext == "paf":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1269 self.add_paf(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1270 dataset_path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1271 outputTrackConfig,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1272 track["conf"]["options"]["paf"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1273 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1274 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1275 logging.warn("Do not know how to handle %s", dataset_ext)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1276 # Return non-human label for use in other fields
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1277 yield outputTrackConfig["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1278
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1279 def add_default_session(self, default_data):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1280 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1281 Add some default session settings: set some assemblies/tracks on/off
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1282
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1283 labels off 1
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1284 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1285 "id": "JJNRSOoj8cPCTR8ZJ7Yne",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1286 "type": "VariantTrack",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1287 "configuration": "vcf_0_merlin.vcf",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1288 "minimized": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1289 "displays": [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1290 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1291 "id": "JOvAkv1bdyz5SAJs3JBby",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1292 "type": "LinearVariantDisplay",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1293 "configuration": {},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1294 "trackShowLabels": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1295 "trackShowDescriptions": false
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1296 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1297 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1298 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1299
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1300 track labels at end of default view
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1301 "hideHeader": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1302 "hideHeaderOverview": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1303 "hideNoTracksActive": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1304 "trackSelectorType": "hierarchical",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1305 "showCenterLine": false,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1306 "showCytobandsSetting": true,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1307 "trackLabels": "hidden",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1308 "showGridlines": true,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1309 "showBookmarkHighlights": true,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1310 "showBookmarkLabels": true
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1311 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1312 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1313 "sessionTracks": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1314 "sessionAssemblies": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1315 "temporaryAssemblies": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1316 "connectionInstances": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1317 "sessionConnections": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1318 "focusedViewId": "n-7YuEPiR5QUtHntU-xcO",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1319 "sessionPlugins": []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1320 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1321 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1322
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1323
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1324 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1325 tracks_data = []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1326
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1327 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1328
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1329 # We need to know the track type from the config.json generated just before
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1330 track_types = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1331 with open(self.config_json_file, "r") as config_file:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1332 config_json = json.load(config_file)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1333 if self.config_json:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1334 config_json.update(self.config_json)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1335
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1336 for track_conf in self.tracksToAdd:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1337 tId = track_conf["trackId"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1338 track_types[tId] = track_conf["type"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1339 style_data = default_data["style"][tId]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1340 logging.warn(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1341 "### defsession for %s got style_data=%s given default_data %s"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1342 % (tId, style_data, default_data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1343 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1344 if "displays" in track_conf:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1345 disp = track_conf["displays"][0]["type"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1346 style_data["type"] = disp
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1347
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1348 style_data["configuration"] = "%s-%s" % (tId, disp)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1349 if track_conf.get("style_labels", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1350 # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1351 # TODO move this to per track displays?
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1352 style_data["labels"] = track_conf["style_labels"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1353 tracks_data.append(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1354 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1355 "type": track_types[tId],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1356 "configuration": tId,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1357 "displays": [style_data],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1358 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1359 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1360
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1361 # The view for the assembly we're adding
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1362 view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1363
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1364 refName = None
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1365 drdict = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1366 "reversed": False,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1367 "assemblyName": self.genome_name,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1368 "start": 1,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1369 "end": 200000,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1370 "refName": "x",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1371 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1372
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1373 if default_data.get("defaultLocation", ""):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1374 ddl = default_data["defaultLocation"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1375 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1376 # allow commas like 100,000 but ignore as integer
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1377 if loc_match:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1378 refName = loc_match.group(1)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1379 drdict["refName"] = refName
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1380 if loc_match.group(2) > "":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1381 drdict["start"] = int(loc_match.group(2).replace(",", ""))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1382 if loc_match.group(3) > "":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1383 drdict["end"] = int(loc_match.group(3).replace(",", ""))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1384 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1385 logging.info(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1386 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1387 % ddl
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1388 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1389 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1390 drdict["refName"] = self.genome_firstcontig
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1391 if drdict.get("refName", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1392 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1393 view_json["displayedRegions"] = [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1394 drdict,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1395 ]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1396
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1397 logging.info("@@@ defaultlocation %s for default session" % drdict)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1398 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1399 logging.info(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1400 "@@@ no contig name found for default session - please add one!"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1401 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1402 session_name = default_data.get("session_name", "New session")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1403 for key, value in mapped_chars.items():
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1404 session_name = session_name.replace(value, key)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1405 # Merge with possibly existing defaultSession (if upgrading a jbrowse instance)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1406 session_json = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1407 if "defaultSession" in config_json:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1408 session_json = config_json["defaultSession"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1409
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1410 session_json["name"] = session_name
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1411
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1412 if "views" not in session_json:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1413 session_json["views"] = []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1414
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1415 session_json["views"].append(view_json)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1416
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1417 config_json["defaultSession"] = session_json
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1418 self.config_json.update(config_json)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1419
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1420 with open(self.config_json_file, "w") as config_file:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1421 json.dump(self.config_json, config_file, indent=2)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1422
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1423 def add_general_configuration(self, data):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1424 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1425 Add some general configuration to the config.json file
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1426 """
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1427
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1428 config_path = self.config_json_file
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1429 if os.path.exists(config_path):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1430 with open(config_path, "r") as config_file:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1431 config_json = json.load(config_file)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1432 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1433 config_json = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1434 if self.config_json:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1435 config_json.update(self.config_json)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1436 config_data = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1437
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1438 config_data["disableAnalytics"] = data.get("analytics", "false") == "true"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1439
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1440 config_data["theme"] = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1441 "palette": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1442 "primary": {"main": data.get("primary_color", "#0D233F")},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1443 "secondary": {"main": data.get("secondary_color", "#721E63")},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1444 "tertiary": {"main": data.get("tertiary_color", "#135560")},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1445 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1446 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1447 "typography": {"fontSize": int(data.get("font_size", 10))},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1448 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1449 if not config_json.get("configuration", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1450 config_json["configuration"] = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1451 config_json["configuration"].update(config_data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1452 self.config_json.update(config_json)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1453 with open(config_path, "w") as config_file:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1454 json.dump(self.config_json, config_file, indent=2)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1455
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1456 def clone_jbrowse(self, realclone=True):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1457 """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now"""
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1458 dest = self.outdir
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1459 if realclone:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1460 self.subprocess_check_call(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1461 ["jbrowse", "create", dest, "-f", "--tag", f"{JB2VER}"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1462 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1463 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1464 shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1465 for fn in [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1466 "asset-manifest.json",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1467 "favicon.ico",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1468 "robots.txt",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1469 "umd_plugin.js",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1470 "version.txt",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1471 "test_data",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1472 ]:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1473 cmd = ["rm", "-rf", os.path.join(dest, fn)]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1474 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1475 cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1476 self.subprocess_check_call(cmd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1477
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1478
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1479 def parse_style_conf(item):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1480 if "type" in item.attrib and item.attrib["type"] in [
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1481 "boolean",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1482 "integer",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1483 ]:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1484 if item.attrib["type"] == "boolean":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1485 return item.text in ("yes", "true", "True")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1486 elif item.attrib["type"] == "integer":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1487 return int(item.text)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1488 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1489 return item.text
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1490
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1491
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1492 if __name__ == "__main__":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1493 parser = argparse.ArgumentParser(description="", epilog="")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1494 parser.add_argument("--xml", help="Track Configuration")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1495 parser.add_argument(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1496 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1497 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1498 parser.add_argument("--outdir", help="Output directory", default="out")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1499 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1500 args = parser.parse_args()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1501 tree = ET.parse(args.xml)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1502 root = tree.getroot()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1503
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1504 # This should be done ASAP
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1505 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1506 # Sometimes this comes as `localhost` without a protocol
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1507 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1508 # so we'll prepend `http://` and hope for the best. Requests *should*
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1509 # be GET and not POST so it should redirect OK
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1510 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1511 jc = JbrowseConnector(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1512 outdir=args.outdir,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1513 jbrowse2path=args.jbrowse2path,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1514 genomes=[
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1515 {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1516 "path": x.attrib["path"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1517 "label": x.attrib["label"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1518 "useuri": x.attrib["useuri"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1519 "meta": metadata_from_node(x.find("metadata")),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1520 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1521 for x in root.findall("metadata/genomes/genome")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1522 ],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1523 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1524 jc.process_genomes()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1525
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1526 # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1527 default_session_data = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1528 "visibility": {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1529 "default_on": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1530 "default_off": [],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1531 },
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1532 "style": {},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1533 "style_labels": {},
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1534 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1535 for track in root.findall("tracks/track"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1536 track_conf = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1537 track_conf["trackfiles"] = []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1538
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1539 is_multi_bigwig = False
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1540 try:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1541 if track.find("options/wiggle/multibigwig") and (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1542 track.find("options/wiggle/multibigwig").text == "True"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1543 ):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1544 is_multi_bigwig = True
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1545 multi_bigwig_paths = []
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1546 except KeyError:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1547 pass
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1548
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1549 trackfiles = track.findall("files/trackFile")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1550 if trackfiles:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1551 for x in track.findall("files/trackFile"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1552 track_conf["label"] = x.attrib["label"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1553 track_conf["useuri"] = x.attrib["useuri"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1554 if is_multi_bigwig:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1555 multi_bigwig_paths.append(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1556 (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1557 x.attrib["label"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1558 x.attrib["useuri"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1559 os.path.realpath(x.attrib["path"]),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1560 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1561 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1562 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1563 if trackfiles:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1564 metadata = metadata_from_node(x.find("metadata"))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1565 track_conf["dataset_id"] = metadata["dataset_id"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1566 if x.attrib["useuri"].lower() == "yes":
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1567 tfa = (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1568 x.attrib["path"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1569 x.attrib["ext"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1570 x.attrib["useuri"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1571 x.attrib["label"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1572 metadata,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1573 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1574 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1575 tfa = (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1576 os.path.realpath(x.attrib["path"]),
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1577 x.attrib["ext"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1578 x.attrib["useuri"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1579 x.attrib["label"],
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1580 metadata,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1581 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1582 track_conf["trackfiles"].append(tfa)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1583
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1584 if is_multi_bigwig:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1585 metadata = metadata_from_node(x.find("metadata"))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1586
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1587 track_conf["trackfiles"].append(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1588 (
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1589 multi_bigwig_paths, # Passing an array of paths to represent as one track
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1590 "bigwig_multiple",
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1591 "MultiBigWig", # Giving an hardcoded name for now
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1592 {}, # No metadata for multiple bigwig
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1593 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1594 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1595 track_conf["category"] = track.attrib["cat"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1596 track_conf["format"] = track.attrib["format"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1597 if track.find("options/style"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1598 track_conf["style"] = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1599 item.tag: parse_style_conf(item) for item in track.find("options/style")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1600 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1601 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1602 track_conf["style"] = {}
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1603 tst = track_conf["style"].get("type", None)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1604 if tst:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1605 track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1606 logging.warn("### got %s for track style" % track_conf["style"])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1607 if track.find("options/style_labels"):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1608 track_conf["style_labels"] = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1609 item.tag: parse_style_conf(item)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1610 for item in track.find("options/style_labels")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1611 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1612 track_conf["conf"] = etree_to_dict(track.find("options"))
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1613 track_conf["category"] = track.attrib["cat"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1614 track_conf["format"] = track.attrib["format"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1615 keys = jc.process_annotations(track_conf)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1616
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1617 if keys:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1618 for key in keys:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1619 default_session_data["visibility"][
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1620 track.attrib.get("visibility", "default_off")
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1621 ].append(key)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1622 if track_conf.get("style", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1623 default_session_data["style"][key] = track_conf["style"]
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1624 if track_conf.get("style_labels", None):
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1625 default_session_data["style_labels"][key] = track_conf.get(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1626 "style_labels", None
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1627 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1628 logging.warn(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1629 "# after process, key=%s def session style = %s"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1630 % (key, default_session_data["style"][key])
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1631 )
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1632 default_session_data["defaultLocation"] = root.find(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1633 "metadata/general/defaultLocation"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1634 ).text
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1635 default_session_data["session_name"] = root.find(
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1636 "metadata/general/session_name"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1637 ).text
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1638 jc.zipOut = root.find("metadata/general/zipOut").text == "true"
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1639 general_data = {
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1640 "analytics": root.find("metadata/general/analytics").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1641 "primary_color": root.find("metadata/general/primary_color").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1642 "secondary_color": root.find("metadata/general/secondary_color").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1643 "tertiary_color": root.find("metadata/general/tertiary_color").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1644 "quaternary_color": root.find("metadata/general/quaternary_color").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1645 "font_size": root.find("metadata/general/font_size").text,
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1646 }
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1647 jc.add_general_configuration(general_data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1648 trackconf = jc.config_json.get("tracks", None)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1649 if trackconf:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
diff changeset
1650 jc.config_json["tracks"].update(jc.tracksToAdd)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1651 else:
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1652 jc.config_json["tracks"] = jc.tracksToAdd
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1653 jc.write_config()
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1654 jc.add_default_session(default_session_data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
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1655 logging.warn("### got default_session_data=%s" % default_session_data)
94264fe60478 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
diff changeset
1656 # jc.text_index() not sure what broke here.