Mercurial > repos > fubar > jbrowse2
annotate jbrowse2.py @ 58:0e592dcaeb7f draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
author | fubar |
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date | Thu, 21 Mar 2024 09:06:52 +0000 |
parents | 94264fe60478 |
children | f807e219cec3 |
rev | line source |
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94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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1 #!/usr/bin/env python |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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2 # change to accumulating all configuration for config.json based on the default from the clone |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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3 import argparse |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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4 import binascii |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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5 import datetime |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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6 import json |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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7 import logging |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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8 import os |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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9 import re |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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10 import shutil |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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11 import struct |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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12 import subprocess |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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13 import tempfile |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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14 import urllib.request |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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15 import xml.etree.ElementTree as ET |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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16 from collections import defaultdict |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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17 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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18 logging.basicConfig(level=logging.INFO) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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19 log = logging.getLogger("jbrowse") |
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b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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20 |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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21 JB2VER = "v2.10.3" |
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b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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22 # version pinned for cloning |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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23 |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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24 TODAY = datetime.datetime.now().strftime("%Y-%m-%d") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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25 GALAXY_INFRASTRUCTURE_URL = None |
38
07849bf248e3
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
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26 |
3
2de9f585505b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty
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27 # version pinned for cloning |
2de9f585505b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit b30d2e277cc360437a02fa812c577c0c8d997cff-dirty
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28 |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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29 mapped_chars = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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30 ">": "__gt__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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31 "<": "__lt__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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32 "'": "__sq__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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33 '"': "__dq__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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34 "[": "__ob__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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35 "]": "__cb__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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36 "{": "__oc__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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37 "}": "__cc__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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38 "@": "__at__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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39 "#": "__pd__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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40 "": "__cn__", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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41 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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42 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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43 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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44 class ColorScaling(object): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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45 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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46 COLOR_FUNCTION_TEMPLATE = """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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47 function(feature, variableName, glyphObject, track) {{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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48 var score = {score}; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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49 {opacity} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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50 return 'rgba({red}, {green}, {blue}, ' + opacity + ')'; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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51 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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52 """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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53 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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54 COLOR_FUNCTION_TEMPLATE_QUAL = r""" |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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55 function(feature, variableName, glyphObject, track) {{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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56 var search_up = function self(sf, attr){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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57 if(sf.get(attr) !== undefined){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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58 return sf.get(attr); |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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59 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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60 if(sf.parent() === undefined) {{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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61 return; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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62 }}else{{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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63 return self(sf.parent(), attr); |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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64 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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65 }}; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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66 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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67 var search_down = function self(sf, attr){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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68 if(sf.get(attr) !== undefined){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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69 return sf.get(attr); |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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70 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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71 if(sf.children() === undefined) {{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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72 return; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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73 }}else{{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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74 var kids = sf.children(); |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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75 for(var child_idx in kids){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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76 var x = self(kids[child_idx], attr); |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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77 if(x !== undefined){{ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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78 return x; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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79 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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80 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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81 return; |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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82 }} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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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); |
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92 var blue = parseInt(result[3], 16); |
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93 if(isNaN(opacity) || opacity < 0){{ opacity = 0; }} |
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94 return 'rgba(' + red + ',' + green + ',' + blue + ',' + opacity + ')'; |
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95 }} |
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96 """ |
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97 |
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98 OPACITY_MATH = { |
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99 "linear": """ |
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100 var opacity = (score - ({min})) / (({max}) - ({min})); |
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101 """, |
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102 "logarithmic": """ |
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103 var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min})); |
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104 """, |
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105 "blast": """ |
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106 var opacity = 0; |
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107 if(score == 0.0) {{ |
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108 opacity = 1; |
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109 }} else {{ |
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110 opacity = (20 - Math.log10(score)) / 180; |
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111 }} |
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112 """, |
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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), |
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118 (31, 120, 180), |
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119 (178, 223, 138), |
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120 (51, 160, 44), |
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121 (251, 154, 153), |
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122 (227, 26, 28), |
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123 (253, 191, 111), |
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124 (255, 127, 0), |
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125 (202, 178, 214), |
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126 (106, 61, 154), |
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127 (255, 255, 153), |
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128 (177, 89, 40), |
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129 (228, 26, 28), |
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130 (55, 126, 184), |
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131 (77, 175, 74), |
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132 (152, 78, 163), |
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133 (255, 127, 0), |
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134 ] |
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135 |
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136 BREWER_DIVERGING_PALLETES = { |
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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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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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159 for line in handle: |
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160 try: |
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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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164 |
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165 if value < min_val: |
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166 min_val = value |
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167 |
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168 if value > max_val: |
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169 max_val = value |
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170 except Exception: |
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171 pass |
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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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179 self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES) |
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180 ] |
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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__": |
23
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235 trackConfig["style"]["color"] = track["scaling"]["scheme"]["color"] |
0
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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 ) |
23
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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__": |
0
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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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281 auto_color = "undefined" |
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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()) |
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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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315 text = t.text.strip() |
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316 if children or t.attrib: |
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317 if text: |
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318 d[t.tag]["#text"] = text |
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319 else: |
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320 d[t.tag] = text |
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321 return d |
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322 |
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323 |
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324 INSTALLED_TO = os.path.dirname(os.path.realpath(__file__)) |
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325 |
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326 |
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327 def metadata_from_node(node): |
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328 metadata = {} |
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329 try: |
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330 if len(node.findall("dataset")) != 1: |
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331 # exit early |
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332 return metadata |
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333 except Exception: |
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334 return {} |
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335 |
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336 for (key, value) in node.findall("dataset")[0].attrib.items(): |
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337 metadata["dataset_%s" % key] = value |
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338 |
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339 if node.findall("history"): |
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340 for (key, value) in node.findall("history")[0].attrib.items(): |
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341 metadata["history_%s" % key] = value |
0
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342 |
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343 if node.findall("metadata"): |
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344 for (key, value) in node.findall("metadata")[0].attrib.items(): |
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345 metadata["metadata_%s" % key] = value |
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346 # Additional Mappings applied: |
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347 metadata[ |
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348 "dataset_edam_format" |
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349 ] = '<a target="_blank" href="http://edamontology.org/{0}">{1}</a>'.format( |
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350 metadata["dataset_edam_format"], metadata["dataset_file_ext"] |
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351 ) |
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352 metadata["history_user_email"] = '<a href="mailto:{0}">{0}</a>'.format( |
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353 metadata["history_user_email"] |
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354 ) |
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355 metadata["hist_name"] = metadata["history_display_name"] |
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356 metadata[ |
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357 "history_display_name" |
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358 ] = '<a target="_blank" href="{galaxy}/history/view/{encoded_hist_id}">{hist_name}</a>'.format( |
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359 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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360 encoded_hist_id=metadata["history_id"], |
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361 hist_name=metadata["history_display_name"], |
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362 ) |
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363 if node.findall("tool"): |
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364 for (key, value) in node.findall("tool")[0].attrib.items(): |
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365 metadata["tool_%s" % key] = value |
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366 metadata[ |
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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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369 galaxy=GALAXY_INFRASTRUCTURE_URL, |
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370 encoded_id=metadata.get("dataset_id", ""), |
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371 tool_id=metadata.get("tool_tool_id", ""), |
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372 tool_version=metadata.get("tool_tool_version", ""), |
19
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373 ) |
0
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374 return metadata |
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375 |
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376 |
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377 class JbrowseConnector(object): |
38
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378 def __init__(self, outdir, jbrowse2path, genomes): |
0
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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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390 self.clone_jbrowse() |
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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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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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396 else: |
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397 log.debug("cd %s && %s", self.outdir, " ".join(command)) |
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398 subprocess.check_call(command, cwd=self.outdir) |
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399 |
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400 def subprocess_popen(self, command): |
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401 log.debug(command) |
0
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402 p = subprocess.Popen( |
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403 command, |
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404 cwd=self.outdir, |
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405 shell=True, |
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406 stdin=subprocess.PIPE, |
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407 stdout=subprocess.PIPE, |
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408 stderr=subprocess.PIPE, |
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|
409 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
410 output, err = p.communicate() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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411 retcode = p.returncode |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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412 if retcode != 0: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
413 log.error(command) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
414 log.error(output) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
415 log.error(err) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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416 raise RuntimeError("Command failed with exit code %s" % (retcode)) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
417 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
418 def subprocess_check_output(self, command): |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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diff
changeset
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419 log.debug(" ".join(command)) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
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420 return subprocess.check_output(command, cwd=self.outdir) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
421 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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422 def symlink_or_copy(self, src, dest): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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423 if "GALAXY_JBROWSE_SYMLINKS" in os.environ and bool( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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424 os.environ["GALAXY_JBROWSE_SYMLINKS"] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
425 ): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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426 cmd = ["ln", "-s", src, dest] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
427 else: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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428 cmd = ["cp", src, dest] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
429 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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430 return self.subprocess_check_call(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
431 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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432 def _prepare_track_style(self, trackDict): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
433 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
434 style_data = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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435 "type": "LinearBasicDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
436 "displayId": "%s-LinearBasicDisplay" % trackDict["trackId"], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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437 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
438 |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
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diff
changeset
|
439 if trackDict.get("displays", None): # use first if multiple like bed |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
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diff
changeset
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440 style_data["type"] = trackDict["displays"][0]["type"] |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
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diff
changeset
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441 style_data["displayId"] = trackDict["displays"][0]["displayId"] |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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changeset
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442 return { |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
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3
diff
changeset
|
443 "displays": [ |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
444 style_data, |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
445 ] |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
446 } |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
447 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
448 def process_genomes(self): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
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449 assemblies = [] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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44
diff
changeset
|
450 useuri = False |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
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451 for i, genome_node in enumerate(self.genome_paths): |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
452 if genome_node["useuri"].strip().lower() == "yes": |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
453 useuri = True |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
454 genome_name = genome_node["meta"]["dataset_dname"].strip() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
455 if len(genome_name.split()) > 1: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
456 genome_name = genome_name.split()[0] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
457 # spaces and cruft break scripts when substituted |
34
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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diff
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458 if genome_name not in self.genome_names: |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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diff
changeset
|
459 # ignore dupes - can have multiple pafs with same references? |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
460 fapath = genome_node["path"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
461 if not useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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462 fapath = os.path.realpath(fapath) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
463 assem = self.make_assembly(fapath, genome_name, useuri) |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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464 assemblies.append(assem) |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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465 self.genome_names.append(genome_name) |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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changeset
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466 if self.genome_name is None: |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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467 self.genome_name = ( |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
fubar
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changeset
|
468 genome_name # first one for all tracks - other than paf |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
469 ) |
53
bdfa6a7c4543
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
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470 self.genome_sequence_adapter = assem["sequence"]["adapter"] |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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471 self.genome_firstcontig = None |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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472 if not useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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changeset
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473 fl = open(fapath, "r").readline() |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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474 fls = fl.strip().split(">") |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
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475 if len(fls) > 1: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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changeset
|
476 fl = fls[1] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
477 if len(fl.split()) > 1: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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changeset
|
478 self.genome_firstcontig = fl.split()[0].strip() |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
479 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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changeset
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480 self.genome_firstcontig = fl |
55
469c0f6d87d7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 0553bb75a96ae401623face516c1cf6e1cfe743f
fubar
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diff
changeset
|
481 else: |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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diff
changeset
|
482 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:
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diff
changeset
|
483 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
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diff
changeset
|
484 self.genome_firstcontig = ( |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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diff
changeset
|
485 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:
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diff
changeset
|
486 ) |
15
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
487 if self.config_json.get("assemblies", None): |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
488 self.config_json["assemblies"] += assemblies |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
489 else: |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
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490 self.config_json["assemblies"] = assemblies |
0
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changeset
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491 |
46
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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492 def make_assembly(self, fapath, gname, useuri): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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493 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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494 faname = fapath |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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495 adapter = { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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496 "type": "BgzipFastaAdapter", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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497 "fastaLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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498 "uri": faname, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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499 "locationType": "UriLocation", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
500 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
|
501 "faiLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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502 "uri": faname + ".fai", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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503 "locationType": "UriLocation", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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504 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
|
505 "gziLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
|
506 "uri": faname + ".gzi", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
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507 "locationType": "UriLocation", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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508 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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changeset
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509 } |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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510 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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511 faname = gname + ".fa.gz" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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512 fadest = os.path.realpath(os.path.join(self.outdir, faname)) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
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513 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % ( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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514 fapath, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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515 fadest, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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516 fadest, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
517 fadest, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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|
518 ) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
519 self.subprocess_popen(cmd) |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
changeset
|
520 |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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521 adapter = { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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522 "type": "BgzipFastaAdapter", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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523 "fastaLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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524 "uri": faname, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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525 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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526 "faiLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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527 "uri": faname + ".fai", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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528 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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529 "gziLocation": { |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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530 "uri": faname + ".gzi", |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
531 }, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
532 } |
53
bdfa6a7c4543
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
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|
533 |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
534 trackDict = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
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|
535 "name": gname, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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536 "sequence": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
537 "type": "ReferenceSequenceTrack", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
538 "trackId": gname, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
539 "adapter": adapter, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
540 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
541 "rendering": {"type": "DivSequenceRenderer"}, |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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542 "displays": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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543 { |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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544 "type": "LinearReferenceSequenceDisplay", |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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545 "displayId": "%s-LinearReferenceSequenceDisplay" % gname, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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546 }, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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547 { |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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56
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548 "type": "LinearGCContentDisplay", |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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|
549 "displayId": "%s-LinearGCContentDisplay" % gname, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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550 }, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
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551 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
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|
552 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
553 return trackDict |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
554 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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555 def add_default_view(self): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
556 cmd = [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
557 "jbrowse", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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558 "set-default-session", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
559 "-s", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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560 self.config_json_file, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
561 "-t", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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562 ",".join(self.trackIdlist), |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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563 "-n", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
564 "JBrowse2 in Galaxy", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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565 "--target", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
566 self.config_json_file, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
567 "-v", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
568 " LinearGenomeView", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
569 ] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
570 self.subprocess_check_call(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
571 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
572 def write_config(self): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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573 with open(self.config_json_file, "w") as fp: |
46
4181e97c70a7
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574 json.dump(self.config_json, fp, indent=2) |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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575 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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576 def text_index(self): |
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577 # Index tracks |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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578 args = [ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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579 "jbrowse", |
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580 "text-index", |
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581 "--target", |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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582 os.path.join(self.outdir, "data"), |
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583 "--assemblies", |
d78175596286
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584 self.genome_name, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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585 ] |
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586 |
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587 tracks = ",".join(self.trackIdlist) |
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588 if tracks: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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589 args += ["--tracks", tracks] |
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590 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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591 self.subprocess_check_call(args) |
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592 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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593 def add_hic(self, data, trackData): |
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594 """ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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595 HiC adapter. |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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596 https://github.com/aidenlab/hic-format/blob/master/HiCFormatV9.md |
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597 for testing locally, these work: |
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598 HiC data is from https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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599 using hg19 reference track as a |
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600 'BgzipFastaAdapter' |
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601 fastaLocation: |
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602 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz', |
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603 faiLocation: |
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604 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.fai', |
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605 gziLocation: |
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606 uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz.gzi', |
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607 Cool will not be likely to be a good fit - see discussion at https://github.com/GMOD/jbrowse-components/issues/2438 |
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608 """ |
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609 tId = trackData["label"] |
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610 # can be served - if public. |
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611 # dsId = trackData["metadata"]["dataset_id"] |
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612 # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) |
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613 useuri = trackData["useuri"].lower() == "yes" |
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614 if useuri: |
4181e97c70a7
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615 uri = data |
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616 else: |
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617 uri = trackData["hic_url"] |
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618 categ = trackData["category"] |
0
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619 trackDict = { |
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620 "type": "HicTrack", |
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621 "trackId": tId, |
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622 "name": uri, |
0
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623 "assemblyNames": [self.genome_name], |
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624 "category": [ |
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625 categ, |
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626 ], |
50
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627 "adapter": { |
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628 "type": "HicAdapter", |
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629 "hicLocation": uri, |
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630 }, |
0
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631 "displays": [ |
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632 { |
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633 "type": "LinearHicDisplay", |
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634 "displayId": "%s-LinearHicDisplay" % tId, |
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635 }, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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636 ], |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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637 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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638 self.tracksToAdd.append(trackDict) |
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639 self.trackIdlist.append(tId) |
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640 |
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641 def add_maf(self, data, trackData): |
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642 """ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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643 from https://github.com/cmdcolin/maf2bed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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644 Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name |
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645 e.g. hg38.chr1 in the sequence identifiers. |
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646 need the reference id - eg hg18, for maf2bed.pl as the first parameter |
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647 """ |
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648 tId = trackData["label"] |
0
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649 mafPlugin = { |
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650 "plugins": [ |
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651 { |
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652 "name": "MafViewer", |
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653 "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js", |
0
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654 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
655 ] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
656 } |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
657 categ = trackData["category"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
658 fname = "%s.bed" % tId |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
659 dest = "%s/%s" % (self.outdir, fname) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
660 gname = self.genome_name |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
661 cmd = [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
662 "bash", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
663 os.path.join(INSTALLED_TO, "convertMAF.sh"), |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
664 data, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
665 gname, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
666 INSTALLED_TO, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
667 dest, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
668 ] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
669 self.subprocess_check_call(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
670 # Construct samples list |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
671 # We could get this from galaxy metadata, not sure how easily. |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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diff
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672 ps = subprocess.Popen(["grep", "^s [^ ]*", "-o", data], stdout=subprocess.PIPE) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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673 output = subprocess.check_output(("sort", "-u"), stdin=ps.stdout) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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674 ps.wait() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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675 outp = output.decode("ascii") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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676 soutp = outp.split("\n") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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677 samp = [x.split("s ")[1] for x in soutp if x.startswith("s ")] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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678 samples = [x.split(".")[0] for x in samp] |
57
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679 logging.warn("### maf convert cmd = %s,\nsamples=%s" % (' '.join(cmd), samples)) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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680 trackDict = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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681 "type": "MafTrack", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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682 "trackId": tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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683 "name": trackData["name"], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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684 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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685 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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|
686 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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687 "adapter": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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688 "type": "MafTabixAdapter", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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689 "samples": samples, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
690 "bedGzLocation": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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691 "uri": fname + ".sorted.bed.gz", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
692 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
693 "index": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
694 "location": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
695 "uri": fname + ".sorted.bed.gz.tbi", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
696 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
697 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
698 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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|
699 "assemblyNames": [self.genome_name], |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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parents:
3
diff
changeset
|
700 "displays": [ |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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3
diff
changeset
|
701 { |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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parents:
3
diff
changeset
|
702 "type": "LinearBasicDisplay", |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
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diff
changeset
|
703 "displayId": "%s-LinearBasicDisplay" % tId, |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
704 }, |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
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|
705 { |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
706 "type": "LinearArcDisplay", |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
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diff
changeset
|
707 "displayId": "%s-LinearArcDisplay" % tId, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
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|
708 }, |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
709 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
710 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
711 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
712 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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713 if self.config_json.get("plugins", None): |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
714 self.config_json["plugins"].append(mafPlugin[0]) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
715 else: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
716 self.config_json.update(mafPlugin) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
717 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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718 def _blastxml_to_gff3(self, xml, min_gap=10): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
719 gff3_unrebased = tempfile.NamedTemporaryFile(delete=False) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
720 cmd = [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
721 "python", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
722 os.path.join(INSTALLED_TO, "blastxml_to_gapped_gff3.py"), |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
723 "--trim", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
724 "--trim_end", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
725 "--include_seq", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
726 "--min_gap", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
727 str(min_gap), |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
728 xml, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
729 ] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
730 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
731 gff3_unrebased.close() |
57
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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732 logging.warn("### blastxml to gff3 cmd = %s" % ' '.join(cmd)) |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
733 return gff3_unrebased.name |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
734 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
735 def add_blastxml(self, data, trackData, blastOpts, **kwargs): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
736 gff3 = self._blastxml_to_gff3(data, min_gap=blastOpts["min_gap"]) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
737 if "parent" in blastOpts and blastOpts["parent"] != "None": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
738 gff3_rebased = tempfile.NamedTemporaryFile(delete=False) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
739 cmd = ["python", os.path.join(INSTALLED_TO, "gff3_rebase.py")] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
740 if blastOpts.get("protein", "false") == "true": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
741 cmd.append("--protein2dna") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
742 cmd.extend([os.path.realpath(blastOpts["parent"]), gff3]) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
743 subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased) |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
744 logging.warn("### gff3rebase cmd = %s" % ' '.join(cmd)) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
745 gff3_rebased.close() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
746 # Replace original gff3 file |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
747 shutil.copy(gff3_rebased.name, gff3) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
748 os.unlink(gff3_rebased.name) |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
749 url = "%s.gff3.gz" % trackData["label"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
750 dest = "%s/%s" % (self.outdir, url) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
751 self._sort_gff(gff3, dest) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
752 tId = trackData["label"] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
753 categ = trackData["category"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
754 trackDict = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
755 "type": "FeatureTrack", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
756 "trackId": tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
757 "name": trackData["name"], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
758 "assemblyNames": [self.genome_name], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
759 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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56
diff
changeset
|
760 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
761 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
762 "adapter": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
763 "type": "Gff3TabixAdapter", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
764 "gffGzLocation": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
765 "uri": url, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
766 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
767 "index": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
768 "location": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
769 "uri": url + ".tbi", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
770 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
771 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
772 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
773 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
774 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
775 "type": "LinearBasicDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
776 "displayId": "%s-LinearBasicDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
777 }, |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
778 { |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
779 "type": "LinearArcDisplay", |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
780 "displayId": "%s-LinearArcDisplay" % tId, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
781 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
782 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
783 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
784 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
785 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
786 os.unlink(gff3) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
787 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
788 def add_bigwig(self, data, trackData): |
15
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
789 """ "type": "LinearWiggleDisplay", |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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parents:
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diff
changeset
|
790 "configuration": {}, |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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diff
changeset
|
791 "selectedRendering": "", |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
14
diff
changeset
|
792 "resolution": 1, |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
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diff
changeset
|
793 "posColor": "rgb(228, 26, 28)", |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
794 "negColor": "rgb(255, 255, 51)", |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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diff
changeset
|
795 "constraints": {} |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
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diff
changeset
|
796 """ |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
797 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
798 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
799 url = data |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
800 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
801 url = "%s.bigwig" % trackData["label"] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
802 # slashes in names cause path trouble |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
|
803 dest = os.path.join(self.outdir, url) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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parents:
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changeset
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804 cmd = ["cp", data, dest] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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parents:
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changeset
|
805 self.subprocess_check_call(cmd) |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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diff
changeset
|
806 bwloc = {"uri": url} |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
807 tId = trackData["label"] |
57
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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diff
changeset
|
808 categ = trackData["category"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
809 trackDict = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
810 "type": "QuantitativeTrack", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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changeset
|
811 "trackId": tId, |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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parents:
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diff
changeset
|
812 "name": trackData["name"], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
813 "category": [ |
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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diff
changeset
|
814 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
815 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
816 "assemblyNames": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
817 self.genome_name, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
818 ], |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
819 "adapter": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
820 "type": "BigWigAdapter", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
821 "bigWigLocation": bwloc, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
822 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
823 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
824 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
825 "type": "LinearWiggleDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
826 "displayId": "%s-LinearWiggleDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
827 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
828 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
829 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
830 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
831 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
832 |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
833 def add_bam(self, data, trackData, bam_index=None, **kwargs): |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
834 tId = trackData["label"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
835 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
836 bindex = bam_index |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
837 categ = trackData["category"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
838 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
839 url = data |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
840 else: |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
841 fname = "%s.bam" % trackData["label"] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
842 dest = "%s/%s" % (self.outdir, fname) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
843 url = fname |
57
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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diff
changeset
|
844 bindex = fname + ".bai" |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
845 self.subprocess_check_call(["cp", data, dest]) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
846 if bam_index is not None and os.path.exists(bam_index): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
847 if not os.path.exists(bindex): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
848 # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
56
diff
changeset
|
849 self.subprocess_check_call(["cp", bam_index, bindex]) |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
850 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
851 # Can happen in exotic condition |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
852 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
853 # => no index generated by galaxy, but there might be one next to the symlink target |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
854 # this trick allows to skip the bam sorting made by galaxy if already done outside |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
855 if os.path.exists(os.path.realpath(data) + ".bai"): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
856 self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
857 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
858 log.warn("Could not find a bam index (.bai file) for %s", data) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
859 trackDict = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
860 "type": "AlignmentsTrack", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
861 "trackId": tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
862 "name": trackData["name"], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
863 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
864 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
865 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
866 "assemblyNames": [self.genome_name], |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
867 "adapter": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
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diff
changeset
|
868 "type": "BamAdapter", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
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diff
changeset
|
869 "bamLocation": {"uri": url}, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
870 "index": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
871 "location": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
872 "uri": bindex, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
873 } |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
874 }, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
875 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
876 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
877 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
878 "type": "LinearAlignmentsDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
879 "displayId": "%s-LinearAlignmentsDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
880 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
881 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
882 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
883 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
884 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
885 |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
886 def add_cram(self, data, trackData, cram_index=None, **kwargs): |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
887 tId = trackData["label"] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
888 categ = trackData["category"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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changeset
|
889 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
890 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
891 url = data |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
892 else: |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
893 fname = "%s.cram" % trackData["label"] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
894 dest = "%s/%s" % (self.outdir, fname) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
895 url = fname |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
896 self.subprocess_check_call(["cp", data, dest]) |
55
469c0f6d87d7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 0553bb75a96ae401623face516c1cf6e1cfe743f
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parents:
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diff
changeset
|
897 if cram_index is not None and os.path.exists(cram_index): |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
898 if not os.path.exists(dest + ".crai"): |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
899 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
900 self.subprocess_check_call( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
901 ["cp", os.path.realpath(cram_index), dest + ".crai"] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
902 ) |
53
bdfa6a7c4543
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents:
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diff
changeset
|
903 else: |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
904 cpath = os.path.realpath(dest) + ".crai" |
53
bdfa6a7c4543
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents:
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diff
changeset
|
905 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
906 logging.debug("executing cmd %s" % " ".join(cmd)) |
53
bdfa6a7c4543
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
fubar
parents:
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diff
changeset
|
907 self.subprocess_check_call(cmd) |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
908 trackDict = { |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
909 "type": "AlignmentsTrack", |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
910 "trackId": tId, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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parents:
17
diff
changeset
|
911 "name": trackData["name"], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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parents:
56
diff
changeset
|
912 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
913 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
914 ], |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
915 "assemblyNames": [self.genome_name], |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
916 "adapter": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
917 "type": "CramAdapter", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
918 "cramLocation": {"uri": url}, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
919 "craiLocation": { |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
920 "uri": url + ".crai", |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
921 }, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
922 "sequenceAdapter": self.genome_sequence_adapter, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
923 }, |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
924 "displays": [ |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
925 { |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
926 "type": "LinearAlignmentsDisplay", |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
927 "displayId": "%s-LinearAlignmentsDisplay" % tId, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
928 }, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
929 ], |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
930 } |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
931 self.tracksToAdd.append(trackDict) |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
932 self.trackIdlist.append(tId) |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
933 |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
934 def add_vcf(self, data, trackData): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
935 tId = trackData["label"] |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
936 # url = "%s/api/datasets/%s/display" % ( |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
937 # self.giURL, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
938 # trackData["metadata"]["dataset_id"], |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
939 # ) |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
940 categ = trackData["category"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
941 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
942 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
943 url = data |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
944 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
945 url = "%s.vcf.gz" % tId |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
946 dest = "%s/%s" % (self.outdir, url) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
947 cmd = "bgzip -c %s > %s" % (data, dest) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
948 self.subprocess_popen(cmd) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
949 cmd = ["tabix", "-f", "-p", "vcf", dest] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
950 self.subprocess_check_call(cmd) |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
951 trackDict = { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
952 "type": "VariantTrack", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
953 "trackId": tId, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
954 "name": trackData["name"], |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
955 "assemblyNames": [self.genome_name], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
956 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
957 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
958 ], |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
959 "adapter": { |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
960 "type": "VcfTabixAdapter", |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
961 "vcfGzLocation": {"uri": url}, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
962 "index": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
963 "location": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
964 "uri": url + ".tbi", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
965 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
966 }, |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
49
diff
changeset
|
967 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
968 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
969 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
970 "type": "LinearVariantDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
971 "displayId": "%s-LinearVariantDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
972 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
973 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
974 "type": "ChordVariantDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
975 "displayId": "%s-ChordVariantDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
976 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
977 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
978 "type": "LinearPairedArcDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
979 "displayId": "%s-LinearPairedArcDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
980 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
981 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
982 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
983 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
984 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
985 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
986 def _sort_gff(self, data, dest): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
987 # Only index if not already done |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
|
988 if not os.path.exists(dest): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
989 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % ( |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
990 data, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
991 dest, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
992 ) # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'" |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
993 self.subprocess_popen(cmd) |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
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994 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest]) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
995 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
996 def _sort_bed(self, data, dest): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
997 # Only index if not already done |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
998 if not os.path.exists(dest): |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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diff
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|
999 cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1000 self.subprocess_popen(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1001 cmd = ["tabix", "-f", "-p", "bed", dest] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1002 self.subprocess_check_call(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1003 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1004 def add_gff(self, data, ext, trackData): |
46
4181e97c70a7
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1005 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
|
1006 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1007 url = trackData["path"] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1008 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
|
1009 url = "%s.%s.gz" % (trackData["label"], ext) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
1010 dest = "%s/%s" % (self.outdir, url) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
1011 self._sort_gff(data, dest) |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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|
1012 tId = trackData["label"] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
1013 categ = trackData["category"] |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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changeset
|
1014 trackDict = { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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diff
changeset
|
1015 "type": "FeatureTrack", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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parents:
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diff
changeset
|
1016 "trackId": tId, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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diff
changeset
|
1017 "name": trackData["name"], |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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parents:
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changeset
|
1018 "assemblyNames": [self.genome_name], |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
1019 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
1020 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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changeset
|
1021 ], |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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parents:
49
diff
changeset
|
1022 "adapter": { |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1023 "type": "Gff3TabixAdapter", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1024 "gffGzLocation": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1025 "uri": url, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1026 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1027 "index": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1028 "location": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1029 "uri": url + ".tbi", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1030 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1031 }, |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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diff
changeset
|
1032 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1033 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1034 { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1035 "type": "LinearBasicDisplay", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1036 "displayId": "%s-LinearBasicDisplay" % tId, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1037 }, |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1038 { |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1039 "type": "LinearArcDisplay", |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1040 "displayId": "%s-LinearArcDisplay" % tId, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1041 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1042 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1043 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1044 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1045 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1046 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1047 def add_bed(self, data, ext, trackData): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1048 tId = trackData["label"] |
57
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
1049 categ = trackData["category"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
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|
1050 useuri = trackData["useuri"].lower() == "yes" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1051 if useuri: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1052 url = data |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
1053 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
1054 url = "%s.%s.gz" % (trackData["label"], ext) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
1055 dest = "%s/%s" % (self.outdir, url) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
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diff
changeset
|
1056 self._sort_bed(data, dest) |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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parents:
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diff
changeset
|
1057 trackDict = { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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|
1058 "type": "FeatureTrack", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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|
1059 "trackId": tId, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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parents:
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diff
changeset
|
1060 "name": trackData["name"], |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
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diff
changeset
|
1061 "assemblyNames": [self.genome_name], |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
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diff
changeset
|
1062 "adapter": { |
57
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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diff
changeset
|
1063 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1064 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
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|
1065 ], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1066 "type": "BedTabixAdapter", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1067 "bedGzLocation": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1068 "uri": url, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1069 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1070 "index": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1071 "location": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1072 "uri": url + ".tbi", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1073 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
1074 }, |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
parents:
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diff
changeset
|
1075 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1076 "displays": [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1077 { |
9
a26c41e304c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
fubar
parents:
7
diff
changeset
|
1078 "type": "LinearBasicDisplay", |
a26c41e304c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
fubar
parents:
7
diff
changeset
|
1079 "displayId": "%s-LinearBasicDisplay" % tId, |
a26c41e304c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
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parents:
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diff
changeset
|
1080 }, |
a26c41e304c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
fubar
parents:
7
diff
changeset
|
1081 { |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
3
diff
changeset
|
1082 "type": "LinearPileupDisplay", |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
fubar
parents:
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diff
changeset
|
1083 "displayId": "%s-LinearPileupDisplay" % tId, |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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changeset
|
1084 }, |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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diff
changeset
|
1085 { |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1086 "type": "LinearArcDisplay", |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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changeset
|
1087 "displayId": "%s-LinearArcDisplay" % tId, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents:
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diff
changeset
|
1088 }, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1089 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1090 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1091 self.tracksToAdd.append(trackDict) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1092 self.trackIdlist.append(tId) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1093 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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changeset
|
1094 def add_paf(self, data, trackData, pafOpts, **kwargs): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1095 tname = trackData["name"] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1096 tId = trackData["label"] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
|
1097 categ = trackData["category"] |
34
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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diff
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|
1098 pgnames = [x.strip() for x in pafOpts["genome_label"].split(",")] |
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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|
1099 pgpaths = [x.strip() for x in pafOpts["genome"].split(",")] |
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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1100 passnames = [self.genome_name] # always first |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1101 for i, gname in enumerate(pgnames): |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1102 if len(gname.split()) > 1: |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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changeset
|
1103 gname = gname.split()[0] |
47
3e53204c2419
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
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|
1104 passnames.append(gname) |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1105 # trouble from spacey names in command lines avoidance |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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diff
changeset
|
1106 if gname not in self.genome_names: |
34
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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|
1107 # ignore if already there - eg for duplicates among pafs. |
57
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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changeset
|
1108 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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changeset
|
1109 "https://" |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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|
1110 ) |
54
d6b0feb22584
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 53aab6394c715dc2d7fdd9188d6c9834e0516b5c
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1111 asstrack = self.make_assembly(pgpaths[i], gname, useuri) |
31
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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1112 self.genome_names.append(gname) |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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1113 if self.config_json.get("assemblies", None): |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1114 self.config_json["assemblies"].append(asstrack) |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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1115 else: |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1116 self.config_json["assemblies"] = [ |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1117 asstrack, |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1118 ] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1119 url = "%s.paf" % (trackData["label"]) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1120 dest = "%s/%s" % (self.outdir, url) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1121 self.symlink_or_copy(os.path.realpath(data), dest) |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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diff
changeset
|
1122 trackDict = { |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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diff
changeset
|
1123 "type": "SyntenyTrack", |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
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diff
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|
1124 "trackId": tId, |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
1125 "assemblyNames": passnames, |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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changeset
|
1126 "category": [ |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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changeset
|
1127 categ, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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changeset
|
1128 ], |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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diff
changeset
|
1129 "name": tname, |
50
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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|
1130 "adapter": { |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
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|
1131 "type": "PAFAdapter", |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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changeset
|
1132 "pafLocation": {"uri": url}, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
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changeset
|
1133 "assemblyNames": passnames, |
f350467f9433
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4
fubar
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changeset
|
1134 }, |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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diff
changeset
|
1135 "displays": [ |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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changeset
|
1136 { |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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changeset
|
1137 "type": "LinearSyntenyDisplay", |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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changeset
|
1138 "displayId": "%s-LinearSyntenyDisplay" % tId, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1139 }, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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|
1140 { |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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|
1141 "type": "DotPlotDisplay", |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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changeset
|
1142 "displayId": "%s-DotPlotDisplay" % tId, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
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diff
changeset
|
1143 }, |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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diff
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|
1144 ], |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1145 } |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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diff
changeset
|
1146 self.tracksToAdd.append(trackDict) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1147 self.trackIdlist.append(tId) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1148 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1149 def process_annotations(self, track): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1150 category = track["category"].replace("__pd__date__pd__", TODAY) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1151 for i, ( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1152 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1153 dataset_ext, |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
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|
1154 useuri, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
1155 track_human_label, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1156 extra_metadata, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1157 ) in enumerate(track["trackfiles"]): |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1158 if not dataset_path.strip().startswith("http"): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
1159 # Unsanitize labels (element_identifiers are always sanitized by Galaxy) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1160 for key, value in mapped_chars.items(): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1161 track_human_label = track_human_label.replace(value, key) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1162 track_human_label = track_human_label.replace(" ", "_") |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1163 outputTrackConfig = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1164 "category": category, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1165 "style": {}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1166 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1167 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1168 outputTrackConfig["key"] = track_human_label |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1169 outputTrackConfig["useuri"] = useuri |
48
460d5b6c5d98
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
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|
1170 outputTrackConfig["path"] = dataset_path |
460d5b6c5d98
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a-dirty
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|
1171 outputTrackConfig["ext"] = dataset_ext |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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diff
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|
1172 |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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diff
changeset
|
1173 outputTrackConfig["trackset"] = track.get("trackset", {}) |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
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|
1174 outputTrackConfig["label"] = "%s_%i_%s" % ( |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
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|
1175 dataset_ext, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
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|
1176 i, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1177 track_human_label, |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
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|
1178 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1179 outputTrackConfig["metadata"] = extra_metadata |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1180 outputTrackConfig["name"] = track_human_label |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1181 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1182 if dataset_ext in ("gff", "gff3"): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1183 self.add_gff( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1184 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1185 dataset_ext, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1186 outputTrackConfig, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1187 ) |
34
2893ef33fba9
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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diff
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|
1188 elif dataset_ext in ("hic", "juicebox_hic"): |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1189 self.add_hic( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1190 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1191 outputTrackConfig, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1192 ) |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
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|
1193 elif dataset_ext in ("cool", "mcool", "scool"): |
30
8f02a84ee278
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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diff
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|
1194 hic_url = "%s_%d.juicebox_hic" % (track_human_label, i) |
29
f728cf0df71d
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|
1195 hic_path = os.path.join(self.outdir, hic_url) |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1196 self.subprocess_check_call( |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
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|
1197 [ |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
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|
1198 "hictk", |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
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|
1199 "convert", |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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|
1200 "-f", |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1201 "--output-fmt", |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1202 "hic", |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1203 dataset_path, |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
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diff
changeset
|
1204 hic_path, |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1205 ] |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
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diff
changeset
|
1206 ) |
29
f728cf0df71d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
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diff
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|
1207 outputTrackConfig["hic_url"] = hic_url |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1208 self.add_hic( |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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diff
changeset
|
1209 hic_path, |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
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changeset
|
1210 outputTrackConfig, |
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
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diff
changeset
|
1211 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1212 elif dataset_ext in ("bed",): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1213 self.add_bed( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1214 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1215 dataset_ext, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1216 outputTrackConfig, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1217 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1218 elif dataset_ext in ("maf",): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1219 self.add_maf( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1220 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1221 outputTrackConfig, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1222 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1223 elif dataset_ext == "bigwig": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1224 self.add_bigwig( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1225 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1226 outputTrackConfig, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1227 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1228 elif dataset_ext == "bam": |
37
7adde511daa1
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
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parents:
35
diff
changeset
|
1229 real_indexes = track["conf"]["options"]["bam"]["bam_index"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1230 self.add_bam( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
1231 dataset_path, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1232 outputTrackConfig, |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1233 bam_index=real_indexes, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1234 ) |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
fubar
parents:
17
diff
changeset
|
1235 elif dataset_ext == "cram": |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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parents:
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diff
changeset
|
1236 real_indexes = track["conf"]["options"]["cram"]["cram_index"] |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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parents:
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diff
changeset
|
1237 self.add_cram( |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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17
diff
changeset
|
1238 dataset_path, |
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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parents:
17
diff
changeset
|
1239 outputTrackConfig, |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1240 cram_index=real_indexes, |
19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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diff
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|
1241 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1242 elif dataset_ext == "blastxml": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1243 self.add_blastxml( |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1244 dataset_path, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1245 outputTrackConfig, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1246 track["conf"]["options"]["blast"], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1247 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1248 elif dataset_ext == "vcf": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1249 self.add_vcf(dataset_path, outputTrackConfig) |
15
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
14
diff
changeset
|
1250 elif dataset_ext == "paf": |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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parents:
14
diff
changeset
|
1251 self.add_paf( |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1252 dataset_path, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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parents:
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diff
changeset
|
1253 outputTrackConfig, |
27
4ff1ed2065cc
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty
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25
diff
changeset
|
1254 track["conf"]["options"]["paf"], |
15
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
fubar
parents:
14
diff
changeset
|
1255 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1256 else: |
29
f728cf0df71d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
fubar
parents:
28
diff
changeset
|
1257 logging.warn("Do not know how to handle %s", dataset_ext) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1258 # Return non-human label for use in other fields |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1259 yield outputTrackConfig["label"] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1260 |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1261 def add_default_session(self, default_data): |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1262 """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1263 Add some default session settings: set some assemblies/tracks on/off |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1264 """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1265 tracks_data = [] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1266 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1267 # TODO using the default session for now, but check out session specs in the future https://github.com/GMOD/jbrowse-components/issues/2708 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1268 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1269 # We need to know the track type from the config.json generated just before |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1270 track_types = {} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1271 with open(self.config_json_file, "r") as config_file: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1272 config_json = json.load(config_file) |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1273 if self.config_json: |
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1274 config_json.update(self.config_json) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1275 |
6
79f7265f90bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9-dirty
fubar
parents:
5
diff
changeset
|
1276 for track_conf in self.tracksToAdd: |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1277 track_types[track_conf["trackId"]] = track_conf["type"] |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1278 tId = track_conf["trackId"] |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1279 #if tId in data["visibility"]["default_on"]: |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1280 style_data = default_data["style"].get(tId, None) |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1281 if not style_data: |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1282 logging.warn("### No style data in default data for %s" % tId) |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1283 style_data = {"type": "LinearBasicDisplay"} |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1284 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:
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diff
changeset
|
1285 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:
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diff
changeset
|
1286 style_data["type"] = disp |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1287 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:
56
diff
changeset
|
1288 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:
56
diff
changeset
|
1289 # 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:
56
diff
changeset
|
1290 # 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:
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diff
changeset
|
1291 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
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parents:
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diff
changeset
|
1292 tracks_data.append( |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1293 { |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1294 "type": track_types[tId], |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1295 "configuration": tId, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1296 "displays": [style_data], |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1297 } |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1298 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1299 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1300 # The view for the assembly we're adding |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1301 view_json = {"type": "LinearGenomeView", "tracks": tracks_data} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1302 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1303 refName = None |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1304 drdict = { |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1305 "reversed": False, |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1306 "assemblyName": self.genome_name, |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1307 "start": 1, |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
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diff
changeset
|
1308 "end": 100000, |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1309 "refName": "x", |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1310 } |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
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diff
changeset
|
1311 |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1312 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:
56
diff
changeset
|
1313 ddl = default_data["defaultLocation"] |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
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19
diff
changeset
|
1314 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) |
27
4ff1ed2065cc
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit d733fb18a02929c9e9959ad30bd0f1368118e924-dirty
fubar
parents:
25
diff
changeset
|
1315 # allow commas like 100,000 but ignore as integer |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1316 if loc_match: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1317 refName = loc_match.group(1) |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1318 drdict["refName"] = refName |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1319 if loc_match.group(2) > "": |
28
9a5c409f33f4
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit e65f2527a97a04173091d28b939e42101582bc56-dirty
fubar
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27
diff
changeset
|
1320 drdict["start"] = int(loc_match.group(2).replace(",", "")) |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1321 if loc_match.group(3) > "": |
28
9a5c409f33f4
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit e65f2527a97a04173091d28b939e42101582bc56-dirty
fubar
parents:
27
diff
changeset
|
1322 drdict["end"] = int(loc_match.group(3).replace(",", "")) |
12
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1323 else: |
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1324 logging.info( |
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1325 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" |
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1326 % ddl |
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1327 ) |
29
f728cf0df71d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
fubar
parents:
28
diff
changeset
|
1328 else: |
f728cf0df71d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
fubar
parents:
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diff
changeset
|
1329 drdict["refName"] = self.genome_firstcontig |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1330 if drdict.get("refName", None): |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1331 # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1332 view_json["displayedRegions"] = [ |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1333 drdict, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1334 ] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1335 |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1336 logging.info("@@@ defaultlocation %s for default session" % drdict) |
12
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1337 else: |
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1338 logging.info( |
13
1d86925dbb4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 873a12803692b0a84814a6dc08331d772d0e5492-dirty
fubar
parents:
12
diff
changeset
|
1339 "@@@ no contig name found for default session - please add one!" |
12
247e17ce504b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4baeb144cafbb61ae0587cce731066129097c168-dirty
fubar
parents:
11
diff
changeset
|
1340 ) |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1341 session_name = default_data.get("session_name", "New session") |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1342 for key, value in mapped_chars.items(): |
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1343 session_name = session_name.replace(value, key) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1344 # Merge with possibly existing defaultSession (if upgrading a jbrowse instance) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1345 session_json = {} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1346 if "defaultSession" in config_json: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1347 session_json = config_json["defaultSession"] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1348 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1349 session_json["name"] = session_name |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1350 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1351 if "views" not in session_json: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1352 session_json["views"] = [] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1353 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1354 session_json["views"].append(view_json) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1355 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1356 config_json["defaultSession"] = session_json |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1357 self.config_json.update(config_json) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1358 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1359 with open(self.config_json_file, "w") as config_file: |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1360 json.dump(self.config_json, config_file, indent=2) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1361 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1362 def add_general_configuration(self, data): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1363 """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1364 Add some general configuration to the config.json file |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1365 """ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1366 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1367 config_path = self.config_json_file |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1368 if os.path.exists(config_path): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1369 with open(config_path, "r") as config_file: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1370 config_json = json.load(config_file) |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1371 else: |
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1372 config_json = {} |
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1373 if self.config_json: |
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
fubar
parents:
9
diff
changeset
|
1374 config_json.update(self.config_json) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1375 config_data = {} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1376 |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
19
diff
changeset
|
1377 config_data["disableAnalytics"] = data.get("analytics", "false") == "true" |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1378 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1379 config_data["theme"] = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1380 "palette": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1381 "primary": {"main": data.get("primary_color", "#0D233F")}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1382 "secondary": {"main": data.get("secondary_color", "#721E63")}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1383 "tertiary": {"main": data.get("tertiary_color", "#135560")}, |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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|
1384 "quaternary": {"main": data.get("quaternary_color", "#FFB11D")}, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1385 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1386 "typography": {"fontSize": int(data.get("font_size", 10))}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1387 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1388 if not config_json.get("configuration", None): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1389 config_json["configuration"] = {} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1390 config_json["configuration"].update(config_data) |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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diff
changeset
|
1391 self.config_json.update(config_json) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1392 with open(config_path, "w") as config_file: |
10
c60b17456297
planemo upload commit 740eeca506257070c95f4e9f1a75911c31db5a04
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diff
changeset
|
1393 json.dump(self.config_json, config_file, indent=2) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1394 |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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changeset
|
1395 def clone_jbrowse(self, realclone=True): |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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1396 """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now""" |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1397 dest = self.outdir |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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|
1398 if realclone: |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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changeset
|
1399 self.subprocess_check_call( |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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diff
changeset
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1400 ["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
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diff
changeset
|
1401 ) |
56
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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diff
changeset
|
1402 else: |
c0097a584a8a
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674
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changeset
|
1403 shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1404 for fn in [ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1405 "asset-manifest.json", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1406 "favicon.ico", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
1407 "robots.txt", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1408 "umd_plugin.js", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1409 "version.txt", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1410 "test_data", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
1411 ]: |
38
07849bf248e3
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
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|
1412 cmd = ["rm", "-rf", os.path.join(dest, fn)] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
1413 self.subprocess_check_call(cmd) |
38
07849bf248e3
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
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1414 cmd = ["cp", os.path.join(INSTALLED_TO, "jb2_webserver.py"), dest] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1415 self.subprocess_check_call(cmd) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1416 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1417 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1418 def parse_style_conf(item): |
57
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diff
changeset
|
1419 if item.text.lower() in ['false','true','yes','no']: |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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|
1420 return item.text.lower in ("yes", "true") |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1421 else: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1422 return item.text |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1423 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1424 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1425 if __name__ == "__main__": |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1426 parser = argparse.ArgumentParser(description="", epilog="") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1427 parser.add_argument("--xml", help="Track Configuration") |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
1428 parser.add_argument( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
changeset
|
1429 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda" |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
1430 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1431 parser.add_argument("--outdir", help="Output directory", default="out") |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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diff
changeset
|
1432 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1") |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
1433 args = parser.parse_args() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1434 tree = ET.parse(args.xml) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1435 root = tree.getroot() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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diff
changeset
|
1436 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1437 # This should be done ASAP |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1438 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1439 # Sometimes this comes as `localhost` without a protocol |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1440 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1441 # so we'll prepend `http://` and hope for the best. Requests *should* |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1442 # be GET and not POST so it should redirect OK |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1443 GALAXY_INFRASTRUCTURE_URL = "http://" + GALAXY_INFRASTRUCTURE_URL |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1444 jc = JbrowseConnector( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
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changeset
|
1445 outdir=args.outdir, |
38
07849bf248e3
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
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|
1446 jbrowse2path=args.jbrowse2path, |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1447 genomes=[ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1448 { |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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|
1449 "path": x.attrib["path"], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
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diff
changeset
|
1450 "label": x.attrib["label"], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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changeset
|
1451 "useuri": x.attrib["useuri"], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
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changeset
|
1452 "meta": metadata_from_node(x.find("metadata")), |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1453 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1454 for x in root.findall("metadata/genomes/genome") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1455 ], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1456 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1457 jc.process_genomes() |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1458 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1459 # .add_default_view() replace from https://github.com/abretaud/tools-iuc/blob/jbrowse2/tools/jbrowse2/jbrowse2.py |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1460 default_session_data = { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1461 "visibility": { |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1462 "default_on": [], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1463 "default_off": [], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1464 }, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1465 "style": {}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1466 "style_labels": {}, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1467 } |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1468 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1469 for track in root.findall("tracks/track"): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1470 track_conf = {} |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1471 track_conf["trackfiles"] = [] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1472 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1473 is_multi_bigwig = False |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1474 try: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1475 if track.find("options/wiggle/multibigwig") and ( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1476 track.find("options/wiggle/multibigwig").text == "True" |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1477 ): |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1478 is_multi_bigwig = True |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1479 multi_bigwig_paths = [] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1480 except KeyError: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1481 pass |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1482 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1483 trackfiles = track.findall("files/trackFile") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1484 if trackfiles: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1485 for x in track.findall("files/trackFile"): |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1486 track_conf["label"] = x.attrib["label"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1487 track_conf["useuri"] = x.attrib["useuri"] |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1488 if is_multi_bigwig: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1489 multi_bigwig_paths.append( |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1490 ( |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1491 x.attrib["label"], |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1492 x.attrib["useuri"], |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1493 os.path.realpath(x.attrib["path"]), |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
fubar
parents:
15
diff
changeset
|
1494 ) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1495 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1496 else: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1497 if trackfiles: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1498 metadata = metadata_from_node(x.find("metadata")) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1499 track_conf["dataset_id"] = metadata["dataset_id"] |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1500 if x.attrib["useuri"].lower() == "yes": |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1501 tfa = ( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1502 x.attrib["path"], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1503 x.attrib["ext"], |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1504 x.attrib["useuri"], |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1505 x.attrib["label"], |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1506 metadata, |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1507 ) |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1508 else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1509 tfa = ( |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1510 os.path.realpath(x.attrib["path"]), |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1511 x.attrib["ext"], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1512 x.attrib["useuri"], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1513 x.attrib["label"], |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1514 metadata, |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1515 ) |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
44
diff
changeset
|
1516 track_conf["trackfiles"].append(tfa) |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1517 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1518 if is_multi_bigwig: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1519 metadata = metadata_from_node(x.find("metadata")) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1520 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1521 track_conf["trackfiles"].append( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1522 ( |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1523 multi_bigwig_paths, # Passing an array of paths to represent as one track |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1524 "bigwig_multiple", |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1525 "MultiBigWig", # Giving an hardcoded name for now |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1526 {}, # No metadata for multiple bigwig |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1527 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1528 ) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1529 track_conf["category"] = track.attrib["cat"] |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1530 track_conf["format"] = track.attrib["format"] |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1531 if track.find("options/style"): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1532 track_conf["style"] = { |
23
39b717d934a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
fubar
parents:
19
diff
changeset
|
1533 item.tag: parse_style_conf(item) for item in track.find("options/style") |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1534 } |
57
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1535 else: |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1536 track_conf["style"] = {} |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1537 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:
56
diff
changeset
|
1538 if tst: |
94264fe60478
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
fubar
parents:
56
diff
changeset
|
1539 track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst) |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1540 if track.find("options/style_labels"): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1541 track_conf["style_labels"] = { |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
6
diff
changeset
|
1542 item.tag: parse_style_conf(item) |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
fubar
parents:
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1543 for item in track.find("options/style_labels") |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1544 } |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1545 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1546 track_conf["conf"] = etree_to_dict(track.find("options")) |
15
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1547 track_conf["category"] = track.attrib["cat"] |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1548 track_conf["format"] = track.attrib["format"] |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1549 keys = jc.process_annotations(track_conf) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1550 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1551 if keys: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1552 for key in keys: |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1553 default_session_data["visibility"][ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1554 track.attrib.get("visibility", "default_off") |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1555 ].append(key) |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1556 if track_conf.get("style", None): |
57
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty
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1557 default_session_data["style"][key] = track_conf["style"] |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1558 if track_conf.get("style_lables", None): |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1559 default_session_data["style_labels"][key] = track_conf.get( |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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|
1560 "style_labels", None |
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1561 ) |
15
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1562 default_session_data["defaultLocation"] = root.find( |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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|
1563 "metadata/general/defaultLocation" |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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|
1564 ).text |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1565 default_session_data["session_name"] = root.find( |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1566 "metadata/general/session_name" |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1567 ).text |
34
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd
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1568 jc.zipOut = root.find("metadata/general/zipOut").text == "true" |
15
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1569 general_data = { |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1570 "analytics": root.find("metadata/general/analytics").text, |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1571 "primary_color": root.find("metadata/general/primary_color").text, |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1572 "secondary_color": root.find("metadata/general/secondary_color").text, |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1573 "tertiary_color": root.find("metadata/general/tertiary_color").text, |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit be2268f4c11d54bdd44789dd88dd9017cad27887-dirty
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|
1574 "quaternary_color": root.find("metadata/general/quaternary_color").text, |
15
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1575 "font_size": root.find("metadata/general/font_size").text, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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|
1576 } |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1577 jc.add_general_configuration(general_data) |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1578 trackconf = jc.config_json.get("tracks", None) |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1579 if trackconf: |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1580 jc.config_json["tracks"].update(jc.tracksToAdd) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1581 else: |
cce8dacb240f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1a20cf06627d429a211427753f223467188dbe7f-dirty
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1582 jc.config_json["tracks"] = jc.tracksToAdd |
9
a26c41e304c3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 1b7e6ba50013775621cbdfdc101152a7f5c5e15b
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diff
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|
1583 jc.write_config() |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1584 jc.add_default_session(default_session_data) |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1585 # jc.text_index() not sure what broke here. |