Mercurial > repos > rmarenco > hubarchivecreator
annotate bigPsl.py @ 20:40469b265ddb draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
| author | yating-l |
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| date | Fri, 20 Jan 2017 17:12:03 -0500 |
| parents | |
| children | 884ee2a71680 |
| rev | line source |
|---|---|
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20
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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1 #!/usr/bin/python |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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2 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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3 import os |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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4 import tempfile |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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5 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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6 from Datatype import Datatype |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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7 from Track import Track |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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8 from TrackDb import TrackDb |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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9 from util import subtools |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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10 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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11 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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12 class bigPsl( Datatype ): |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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13 def __init__(self, input_bigpsl_false_path, data_bigpsl): |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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14 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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15 super(bigPsl, self).__init__() |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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16 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents:
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17 self.input_bigpsl_false_path = input_bigpsl_false_path |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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18 self.name_bigpsl = data_bigpsl["name"] |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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19 self.priority = data_bigpsl["order_index"] |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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20 self.track_color = data_bigpsl["track_color"] |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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21 # TODO: Think about how to avoid repetition of the group_name everywhere |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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diff
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22 self.group_name = data_bigpsl["group_name"] |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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23 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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24 #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed") |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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diff
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25 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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26 # Sort processing |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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diff
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27 #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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28 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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29 # bedToBigBed processing |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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diff
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30 # TODO: Change the name of the bb, to tool + genome + .bb |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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diff
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31 trackName = "".join( ( self.name_bigpsl, '.bb' ) ) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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32 myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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33 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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34 auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as') |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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35 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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36 with open(myBigBedFilePath, 'w') as bigBedFile: |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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37 subtools.bedToBigBed(self.input_bigpsl_false_path, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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38 self.chromSizesFile.name, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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39 bigBedFile.name, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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40 typeOption='bed12+12', |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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41 tab='True', |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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42 autoSql=auto_sql_option) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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43 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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44 # Create the Track Object |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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45 self.createTrack(file_path=trackName, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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46 track_name=trackName, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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47 long_label=self.name_bigpsl, track_type='bigBed 12 +', visibility='dense', |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
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48 priority=self.priority, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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49 track_file=myBigBedFilePath, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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50 track_color=self.track_color, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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51 group_name=self.group_name) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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52 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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53 # dataURL = "tracks/%s" % trackName |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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54 # |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
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55 # trackDb = TrackDb( |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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56 # trackName=trackName, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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57 # longLabel=self.name_bed_simple_repeats, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents:
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58 # shortLabel=self.getShortName( self.name_bed_simple_repeats ), |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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59 # trackDataURL=dataURL, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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60 # trackType='bigBed 4 +', |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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61 # visibility='dense', |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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62 # priority=self.priority, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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63 # ) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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64 # |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents:
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65 # self.track = Track( |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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66 # trackFile=myBigBedFilePath, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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67 # trackDb=trackDb, |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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68 # ) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents:
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69 |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
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70 print("- bigPsl %s created" % self.name_bigpsl) |
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40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
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parents:
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71 #print("- %s created in %s" % (trackName, myBigBedFilePath)) |