# HG changeset patch
# User yating-l
# Date 1482438747 18000
# Node ID be8fd2f24c603f7feb6f4da7f5f153f4a6cf8966
# Parent  dd1e233e16a11b8bcae449ed319b4ed06dd78fa0
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit e2db8aa3672f1222b415716054bfb3c5ccd132a1-dirty

diff -r dd1e233e16a1 -r be8fd2f24c60 Bam.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Bam.pyc
Binary file Bam.pyc has changed
diff -r dd1e233e16a1 -r be8fd2f24c60 Bed.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Bed.pyc
Binary file Bed.pyc has changed
diff -r dd1e233e16a1 -r be8fd2f24c60 BedSimpleRepeats.py
diff -r dd1e233e16a1 -r be8fd2f24c60 BedSimpleRepeats.pyc
Binary file BedSimpleRepeats.pyc has changed
diff -r dd1e233e16a1 -r be8fd2f24c60 BedSpliceJunctions.py
--- a/BedSpliceJunctions.py	Thu Dec 22 14:21:03 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-#!/usr/bin/python
-
-import os
-import tempfile
-
-from Datatype import Datatype
-from Track import Track
-from TrackDb import TrackDb
-from util import subtools
-
-
-class BedSpliceJunctions( Datatype ):
-    def __init__(self, input_bed_splice_junctions_false_path, data_bed_splice_junctions):
-
-        super(BedSpliceJunctions, self).__init__()
-
-        self.input_bed_splice_junctions_false_path = input_bed_splice_junctions_false_path
-        self.name_bed_splice_junctions = data_bed_splice_junctions["name"]
-        self.priority = data_bed_splice_junctions["order_index"]
-        self.track_color = data_bed_splice_junctions["track_color"]
-        # TODO: Think about how to avoid repetition of the group_name everywhere
-        self.group_name = data_bed_splice_junctions["group_name"]
-
-        sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
-
-        # Sort processing
-        subtools.sort(self.input_bed_splice_junctions_false_path, sortedBedFile.name)
-
-        # bedToBigBed processing
-        # TODO: Change the name of the bb, to tool + genome + .bb
-        trackName = "".join( ( self.name_bed_splice_junctions, '.bb' ) )
-        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
-
-        auto_sql_option = os.path.join(self.tool_directory, 'spliceJunctions.as')
-
-        with open(myBigBedFilePath, 'w') as bigBedFile:
-            subtools.bedToBigBed(sortedBedFile.name,
-                                 self.chromSizesFile.name,
-                                 bigBedFile.name,
-                                 typeOption='bed12+1',
-                                 autoSql=auto_sql_option)
-
-        # Create the Track Object
-        self.createTrack(file_path=trackName,
-                         track_name=trackName,
-                         long_label=self.name_bed_splice_junctions, track_type='bigBed 12 +', visibility='dense',
-                         priority=self.priority,
-                         track_file=myBigBedFilePath,
-                         track_color=self.track_color,
-                         group_name=self.group_name)
-
-        # dataURL = "tracks/%s" % trackName
-        #
-        # trackDb = TrackDb(
-        #     trackName=trackName,
-        #     longLabel=self.name_bed_simple_repeats,
-        #     shortLabel=self.getShortName( self.name_bed_simple_repeats ),
-        #     trackDataURL=dataURL,
-        #     trackType='bigBed 4 +',
-        #     visibility='dense',
-        #     priority=self.priority,
-        # )
-        #
-        # self.track = Track(
-        #     trackFile=myBigBedFilePath,
-        #     trackDb=trackDb,
-        # )
-
-        print("- Bed splice junctions %s created" % self.name_bed_splice_junctions)
-        #print("- %s created in %s" % (trackName, myBigBedFilePath))
diff -r dd1e233e16a1 -r be8fd2f24c60 BedSpliceJunctions.pyc
Binary file BedSpliceJunctions.pyc has changed
diff -r dd1e233e16a1 -r be8fd2f24c60 BigWig.py
diff -r dd1e233e16a1 -r be8fd2f24c60 BigWig.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 Datatype.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Datatype.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 Gff3.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Gff3.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 Gtf.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Gtf.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 LICENSE.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 Psl.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Psl.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 Track.py
diff -r dd1e233e16a1 -r be8fd2f24c60 Track.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 TrackDb.py
diff -r dd1e233e16a1 -r be8fd2f24c60 TrackDb.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 TrackHub.py
diff -r dd1e233e16a1 -r be8fd2f24c60 TrackHub.pyc
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diff -r dd1e233e16a1 -r be8fd2f24c60 __init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 bigGenePred.as
diff -r dd1e233e16a1 -r be8fd2f24c60 bigPsl.as
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/Makefile
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/.buildinfo
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diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/.buildinfo
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/_modules/hubArchiveCreator.html
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diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/_static/websupport.js
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/code.html
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/genindex.html
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/index.html
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/objects.inv
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/py-modindex.html
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/search.html
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/_build/html/searchindex.js
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/code.rst
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/conf.py
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/index.rst
diff -r dd1e233e16a1 -r be8fd2f24c60 doc/make.bat
diff -r dd1e233e16a1 -r be8fd2f24c60 hubArchiveCreator.py
--- a/hubArchiveCreator.py	Thu Dec 22 14:21:03 2016 -0500
+++ b/hubArchiveCreator.py	Thu Dec 22 15:32:27 2016 -0500
@@ -18,7 +18,6 @@
 # Internal dependencies
 from Bam import Bam
 from BedSimpleRepeats import BedSimpleRepeats
-from BedSpliceJunctions import BedSpliceJunctions
 from Bed import Bed
 from BigWig import BigWig
 from util.Fasta import Fasta
@@ -47,9 +46,6 @@
     # Bed4+12 (TrfBig)
     parser.add_argument('--bedSimpleRepeats', action='append', help='Bed4+12 format, using simpleRepeats.as')
 
-    # Bed12+1 (regtools)
-    parser.add_argument('--bedSpliceJunctions', action='append', help='Bed12+1 format, using spliceJunctions.as')
-
     # Generic Bed (Blastx transformed to bed)
     parser.add_argument('--bed', action='append', help='Bed generic format')
 
@@ -117,7 +113,6 @@
     array_inputs_bam = args.bam
     array_inputs_bed_generic = args.bed
     array_inputs_bed_simple_repeats = args.bedSimpleRepeats
-    array_inputs_bed_splice_junctions = args.bedSpliceJunctions
     array_inputs_bigwig = args.bigwig
     array_inputs_gff3 = args.gff3
     array_inputs_gtf = args.gtf
@@ -144,7 +139,6 @@
                         (array_inputs_bed_generic, Bed),
                         (array_inputs_bigwig, BigWig),
                         (array_inputs_bed_simple_repeats, BedSimpleRepeats),
-                        (array_inputs_bed_splice_junctions, BedSpliceJunctions),
                         (array_inputs_gff3, Gff3),
                         (array_inputs_gtf, Gtf),
                         (array_inputs_psl, Psl)]:
diff -r dd1e233e16a1 -r be8fd2f24c60 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Thu Dec 22 14:21:03 2016 -0500
+++ b/hubArchiveCreator.xml	Thu Dec 22 15:32:27 2016 -0500
@@ -111,11 +111,6 @@
                         #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
                                                 extra_data_dict)
                     #end if
-                    #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
-                        --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
-                        #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
-                                                extra_data_dict)
-                    #end if
                 #end if
                 #if $f.formatChoice.format_select == "psl"
                     --psl $f.formatChoice.PSL
@@ -211,7 +206,6 @@
                             <param name="bed_select" type="select" label="Bed Choice">
                                 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
                                 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
-                                <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
                             </param>
                             <when value="bed_generic">
                                 <param
@@ -230,14 +224,6 @@
                                         label="Bed Simple Repeats (Bed4+12) File"
                                 />
                             </when>
-                            <when value="bed_splice_junctions_option">
-                                <param
-                                        format="bed"
-                                        name="BED_splice_junctions"
-                                        type="data"
-                                        label="Bed Splice Junctions (Bed12+1) File"
-                                />
-                            </when>
                         </conditional>
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -456,7 +442,6 @@
                 />
             </output>
         </test>
-        
 
         <!-- Test with Psl -->
         <test>
diff -r dd1e233e16a1 -r be8fd2f24c60 spliceJunctions.as
--- a/spliceJunctions.as	Thu Dec 22 14:21:03 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-table spliceJunctions
-"Predicted splice junctions"
-    (
-    string chrom;      "Reference sequence chromosome or scaffold"
-    uint   chromStart; "Start position in chromosome"
-    uint   chromEnd;   "End position in chromosome"
-    string name;       "Name of item"
-    uint   score;      "Score from 0-1000"
-    char[1] strand;    "+ or -"
-    uint thickStart;   "Start of where display should be thick (start codon)"
-    uint thickEnd;     "End of where display should be thick (stop codon)"
-    uint reserved;     "Used as itemRgb as of 2004-11-22"
-    int blockCount;    "Number of blocks"
-    int[blockCount] blockSizes; "Comma separated list of block sizes"
-    int[blockCount] chromStarts; "Start positions relative to chromStart"
-    uint junctionScore;   "Number of reads supporting the splice junction"
-    )
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/display.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/genomesAssembly/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/genomesAssembly/layout.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/groupsTxt/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/groupsTxt/layout.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/hubDescription/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/hubDescription/layout.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/hubTxt/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/hubTxt/layout.txt
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diff -r dd1e233e16a1 -r be8fd2f24c60 templates/trackDb/__init__.py
diff -r dd1e233e16a1 -r be8fd2f24c60 templates/trackDb/layout.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/all_datatypes/__main__.log
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/all_datatypes/all_datatypes_trackhub.html
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diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig
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diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb
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diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_generic/inputs/TBLASTN_Alignment_to_proteins.bed
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diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/Dbia3.html
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diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/Dbia3/description.html
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/Dbia3/groups.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/Dbia3/trackDb.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/genomes.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_simple_repeats/myHub/hub.txt
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_splice_junctions/__main__.log
--- a/test-data/bed_splice_junctions/__main__.log	Thu Dec 22 14:21:03 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
-DEBUG:root:#### Welcome in HubArchiveCreator Debug Mode ####
-
diff -r dd1e233e16a1 -r be8fd2f24c60 test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed
--- a/test-data/bed_splice_junctions/inputs/Splice_Junctions_by_regtools.bed	Thu Dec 22 14:21:03 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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