# HG changeset patch
# User yating-l
# Date 1492023933 14400
# Node ID 884ee2a7168028198d8e96e5ddf054ce285f983c
# Parent  40469b265ddb04c1e17fbca5a4a85e6591620453
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty

diff -r 40469b265ddb -r 884ee2a71680 Bam.py
--- a/Bam.py	Fri Jan 20 17:12:03 2017 -0500
+++ b/Bam.py	Wed Apr 12 15:05:33 2017 -0400
@@ -12,7 +12,7 @@
 from Datatype import Datatype
 from Track import Track
 from TrackDb import TrackDb
-from util import subtools
+
 
 
 class Bam( Datatype ):
diff -r 40469b265ddb -r 884ee2a71680 Bam.pyc
Binary file Bam.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 Bed.pyc
Binary file Bed.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 BedBlastAlignments.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BedBlastAlignments.py	Wed Apr 12 15:05:33 2017 -0400
@@ -0,0 +1,73 @@
+#!/usr/bin/python
+
+import os
+import tempfile
+import string
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class BedBlastAlignments( Datatype ):
+    def __init__(self, input_bed_blast_alignments_false_path, data_bed_blast_alignments):
+
+        super(BedBlastAlignments, self).__init__()
+
+        self.input_bed_blast_alignments_false_path = input_bed_blast_alignments_false_path
+        self.name_bed_blast_alignments = data_bed_blast_alignments["name"]
+        self.priority = data_bed_blast_alignments["order_index"]
+        self.track_color = data_bed_blast_alignments["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bed_blast_alignments["group_name"]
+
+        #sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
+
+        # Sort processing
+        #subtools.sort(self.input_bigpsl_false_path, sortedBedFile.name)
+
+        # bedToBigBed processing
+        # TODO: Change the name of the bb, to tool + genome + .bb
+        trackName = "".join( ( self.name_bed_blast_alignments, '.bb' ) )
+
+        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
+
+        auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
+
+        with open(myBigBedFilePath, 'w') as bigBedFile:
+            subtools.bedToBigBed(self.input_bed_blast_alignments_false_path,
+                                 self.chromSizesFile.name,
+                                 bigBedFile.name,
+                                 typeOption='bed12+12',
+                                 tab='True',
+                                 autoSql=auto_sql_option)
+
+        self.createTrack(file_path=trackName,
+                         track_name=trackName,
+                         long_label=self.name_bed_blast_alignments, 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 Blast alignments %s created" % self.name_bed_blast_alignments)
+        #print("- %s created in %s" % (trackName, myBigBedFilePath))
diff -r 40469b265ddb -r 884ee2a71680 BedBlastAlignments.pyc
Binary file BedBlastAlignments.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 BedSimpleRepeats.pyc
Binary file BedSimpleRepeats.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 BedSpliceJunctions.pyc
Binary file BedSpliceJunctions.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 BigWig.pyc
Binary file BigWig.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 Datatype.py
--- a/Datatype.py	Fri Jan 20 17:12:03 2017 -0500
+++ b/Datatype.py	Wed Apr 12 15:05:33 2017 -0400
@@ -95,8 +95,11 @@
         rgb_array = [int(hexa_without_sharp[i:i+2], 16) for i in (0, 2, 4)]
         rgb_ucsc = ','.join(map(str, rgb_array))
 
+        #sanitize the track_name
+        sanitized_name = subtools.fixName(track_name)
+        
         track_db = TrackDb(
-                trackName=track_name,
+                trackName=sanitized_name,
                 longLabel=long_label,
                 shortLabel=short_label,
                 trackDataURL=data_url,
diff -r 40469b265ddb -r 884ee2a71680 Datatype.pyc
Binary file Datatype.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 bigPsl.py
--- a/bigPsl.py	Fri Jan 20 17:12:03 2017 -0500
+++ b/bigPsl.py	Wed Apr 12 15:05:33 2017 -0400
@@ -2,6 +2,7 @@
 
 import os
 import tempfile
+import string
 
 from Datatype import Datatype
 from Track import Track
@@ -29,6 +30,7 @@
         # bedToBigBed processing
         # TODO: Change the name of the bb, to tool + genome + .bb
         trackName = "".join( ( self.name_bigpsl, '.bb' ) )
+
         myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
 
         auto_sql_option = os.path.join(self.tool_directory, 'bigPsl.as')
@@ -41,15 +43,15 @@
                                  tab='True',
                                  autoSql=auto_sql_option)
 
-        # Create the Track Object
         self.createTrack(file_path=trackName,
                          track_name=trackName,
-                         long_label=self.name_bigpsl, track_type='bigBed 12 +', visibility='dense',
+                         long_label=self.name_bigpsl, track_type='bigPsl', visibility='dense',
                          priority=self.priority,
                          track_file=myBigBedFilePath,
                          track_color=self.track_color,
                          group_name=self.group_name)
 
+
         # dataURL = "tracks/%s" % trackName
         #
         # trackDb = TrackDb(
diff -r 40469b265ddb -r 884ee2a71680 bigPsl.pyc
Binary file bigPsl.pyc has changed
diff -r 40469b265ddb -r 884ee2a71680 hubArchiveCreator.py
--- a/hubArchiveCreator.py	Fri Jan 20 17:12:03 2017 -0500
+++ b/hubArchiveCreator.py	Wed Apr 12 15:05:33 2017 -0400
@@ -28,6 +28,7 @@
 from Psl import Psl
 from TrackHub import TrackHub
 from bigPsl import bigPsl
+from BedBlastAlignments import BedBlastAlignments
 
 # TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort
 
@@ -54,8 +55,11 @@
     # Generic Bed (Blastx transformed to bed)
     parser.add_argument('--bed', action='append', help='Bed generic format')
 
-    # Bed12+12 (tblastn)
-    parser.add_argument('--bigpsl', action='append', help='bigPsl format')
+    # BigPsl (blat alignment)
+    parser.add_argument('--bigpsl', action='append', help='bigPsl format, using bigPsl.as')
+
+    # Bed12+12 (tblastn alignment)
+    parser.add_argument('--bedBlastAlignments', action='append', help='Bed12+12 format, using bigPsl.as')
 
     # BigWig Management
     parser.add_argument('--bigwig', action='append', help='BigWig format')
@@ -127,6 +131,7 @@
     array_inputs_gtf = args.gtf
     array_inputs_psl = args.psl
     array_inputs_bigpsl = args.bigpsl
+    array_inputs_bed_blast_alignments = args.bedBlastAlignments
 
     outputFile = args.output
 
@@ -153,7 +158,8 @@
                         (array_inputs_gff3, Gff3),
                         (array_inputs_gtf, Gtf),
                         (array_inputs_psl, Psl),
-                        (array_inputs_bigpsl, bigPsl)]:
+                        (array_inputs_bigpsl, bigPsl),
+                        (array_inputs_bed_blast_alignments, BedBlastAlignments)]:
         if inputs:
             all_datatype_dictionary.update(create_ordered_datatype_objects(datatype_class, inputs, inputs_data))
 
diff -r 40469b265ddb -r 884ee2a71680 hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Fri Jan 20 17:12:03 2017 -0500
+++ b/hubArchiveCreator.xml	Wed Apr 12 15:05:33 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0">
+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
     <description>
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
@@ -99,10 +99,10 @@
                         #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
                                                 extra_data_dict)
                     #end if
-                    #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option"
-                        --bigpsl $f.formatChoice.bedChoice.bigPsl
-                        #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final,
-                                                extra_data_dict)
+                    #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
+                        --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,                              
+                                             extra_data_dict)
                     #end if
                 #end if
                 #if $f.formatChoice.format_select == "psl"
@@ -126,6 +126,11 @@
                     #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
                                              extra_data_dict)
                 #end if
+                #if $f.formatChoice.format_select == "bigpsl"
+                    --bigpsl $f.formatChoice.BIGPSL
+                    #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final,                       
+                                            extra_data_dict)
+                #end if
             #end for
         #end for
 
@@ -176,6 +181,7 @@
                         <option value="bigwig">BIGWIG</option>
                         <option value="gff3">GFF3</option>
                         <option value="gtf">GTF</option>
+                        <option value="bigpsl">BigPsl</option>
                     </param>
 
                     <when value="bam">
@@ -193,14 +199,14 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                    </when>
+                    </when>     
                     <when value="bed">
                         <conditional name="bedChoice">
                             <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>
-                                <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option>
+                                <option value="bed_blast_alignment_option">BED Blast alignments (bed12+12 / bigPsl.as)</option>
                             </param>
                             <when value="bed_generic">
                                 <param
@@ -227,12 +233,12 @@
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
                             </when>
-                            <when value="bigpsl_option">
+                            <when value="bed_blast_alignment_option">
                                 <param
                                         format="bed"
-                                        name="bigPsl"
+                                        name="BED_blast_alignment"
                                         type="data"
-                                        label="bigPsl (Bed12+12) File"
+                                        label="Bed Blast Alignments (Bed12+12) File"
                                 />
                             </when>
                         </conditional>
@@ -304,6 +310,21 @@
                             </sanitizer>
                         </param>
                     </when>
+                    <when value="bigpsl">
+                        <param 
+                                format="bigpsl"
+                                name="BIGPSL"
+                                type="data"
+                                label="bigPsl File"
+                        />
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>   
                 </conditional>
             </repeat>
         </repeat>
diff -r 40469b265ddb -r 884ee2a71680 util/subtools.py
--- a/util/subtools.py	Fri Jan 20 17:12:03 2017 -0500
+++ b/util/subtools.py	Wed Apr 12 15:05:33 2017 -0400
@@ -10,6 +10,7 @@
 import os
 import subprocess
 import sys
+import string
 
 class PopenError(Exception):
     def __init__(self, cmd, error, return_code):
@@ -243,3 +244,13 @@
 
     p = _handleExceptionAndCheckCall(array_call)
     return p
+
+#santitize trackName. Because track name must begin with a letter and
+# contain only the following chars: [a-zA-Z0-9_].
+# See the "track" Common settings at:
+#https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#bigPsl_-_Pairwise_Alignments
+def fixName(filename):
+    valid_chars = "_%s%s" % (string.ascii_letters, string.digits)
+    sanitize_name = ''.join([c if c in valid_chars else '_' for c in filename])
+    sanitize_name = "gonramp_" + sanitize_name
+    return sanitize_name
diff -r 40469b265ddb -r 884ee2a71680 util/subtools.pyc
Binary file util/subtools.pyc has changed