# HG changeset patch
# User rmarenco
# Date 1475262864 14400
# Node ID c02720d1afee66a6a3d53b011e462c54cbc0d149
# Parent  3233451a3bd6e188873b6b7d03f4f9210ff1e3e2
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf

diff -r 3233451a3bd6 -r c02720d1afee Bam.py
--- a/Bam.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Bam.py	Fri Sep 30 15:14:24 2016 -0400
@@ -32,12 +32,11 @@
 
         self.priority = self.data_bam["order_index"]
         self.index_bam = self.data_bam["index"]
-        # TODO: Think about how to avoir repetition of the color treatment
+        # TODO: Think about how to avoid repetition of the color treatment
         self.track_color = self.data_bam["track_color"]
 
-        logging.debug("Color of bam: {0}".format(self.track_color))
-
-        #print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = self.data_bam["group_name"]
 
         # First: Add the bam file
         # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
@@ -55,7 +54,9 @@
                          track_name=self.name_bam,
                          long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
                          track_file=bam_index_file_path,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name
+                         )
         #
         # dataURL = "tracks/%s" % self.name_bam
         #
diff -r 3233451a3bd6 -r c02720d1afee Bam.pyc
Binary file Bam.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Bed.py
--- a/Bed.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Bed.py	Fri Sep 30 15:14:24 2016 -0400
@@ -24,6 +24,9 @@
         self.name_bed_generic = self.data_bed_generic["name"]
         self.priority = self.data_bed_generic["order_index"]
         self.track_color = self.data_bed_generic["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = self.data_bed_generic["group_name"]
+
 
         # Sort processing
         subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
@@ -44,7 +47,8 @@
                          long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
                          priority=self.priority,
                          track_file=myBigBedFilePath,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         # dataURL = "tracks/%s" % trackName
         #
diff -r 3233451a3bd6 -r c02720d1afee Bed.pyc
Binary file Bed.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee BedSimpleRepeats.py
--- a/BedSimpleRepeats.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/BedSimpleRepeats.py	Fri Sep 30 15:14:24 2016 -0400
@@ -18,6 +18,8 @@
         self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
         self.priority = data_bed_simple_repeats["order_index"]
         self.track_color = data_bed_simple_repeats["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bed_simple_repeats["group_name"]
 
         sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
 
@@ -44,7 +46,8 @@
                          long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
                          priority=self.priority,
                          track_file=myBigBedFilePath,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         # dataURL = "tracks/%s" % trackName
         #
diff -r 3233451a3bd6 -r c02720d1afee BedSimpleRepeats.pyc
Binary file BedSimpleRepeats.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee BigWig.py
--- a/BigWig.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/BigWig.py	Fri Sep 30 15:14:24 2016 -0400
@@ -19,6 +19,8 @@
         self.name_bigwig = data_bigwig["name"]
         self.priority = data_bigwig["order_index"]
         self.track_color = data_bigwig["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_bigwig["group_name"]
 
         #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig )
 
@@ -34,7 +36,8 @@
                          track_type='bigWig', visibility='full',
                          priority=self.priority,
                          track_file=myBigWigFilePath,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         # dataURL = "tracks/%s" % trackName
         #
diff -r 3233451a3bd6 -r c02720d1afee BigWig.pyc
Binary file BigWig.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Datatype.py
--- a/Datatype.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Datatype.py	Fri Sep 30 15:14:24 2016 -0400
@@ -76,7 +76,7 @@
                     file_path=None,
                     track_name=None, long_label=None, thick_draw_item='off',
                     short_label=None, track_type=None, visibility=None, priority=None,
-                    track_file=None, track_color='#000000'):
+                    track_file=None, track_color='#000000', group_name="Default"):
 
         # TODO: Remove the hardcoded "tracks" by the value used as variable from myTrackFolderPath
         data_url = "tracks/%s" % file_path
@@ -104,7 +104,8 @@
                 visibility=visibility,
                 thickDrawItem=thick_draw_item,
                 priority=priority,
-                track_color=rgb_ucsc
+                track_color=rgb_ucsc,
+                group_name=group_name
         )
 
         # Return the Bam Track Object
diff -r 3233451a3bd6 -r c02720d1afee Datatype.pyc
Binary file Datatype.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Gff3.py
--- a/Gff3.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Gff3.py	Fri Sep 30 15:14:24 2016 -0400
@@ -20,6 +20,8 @@
         self.name_gff3 = data_gff3["name"]
         self.priority = data_gff3["order_index"]
         self.track_color = data_gff3["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_gff3["group_name"]
 
         # TODO: See if we need these temporary files as part of the generated files
         unsorted_genePred_file = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
@@ -59,6 +61,7 @@
                          track_type='bigGenePred', visibility='dense',
                          priority=self.priority,
                          track_file=myBigBedFilePath,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         print("- Gff3 %s created" % self.name_gff3)
diff -r 3233451a3bd6 -r c02720d1afee Gff3.pyc
Binary file Gff3.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Gtf.py
--- a/Gtf.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Gtf.py	Fri Sep 30 15:14:24 2016 -0400
@@ -21,6 +21,8 @@
         self.name_gtf = data_gtf["name"]
         self.priority = data_gtf["order_index"]
         self.track_color = data_gtf["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_gtf["group_name"]
 
         #print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
 
@@ -61,6 +63,7 @@
                          long_label=self.name_gtf, track_type='bigGenePred',
                          visibility='dense', priority=self.priority,
                          track_file=myBigBedFilePath,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         print("- Gtf %s created" % self.name_gtf)
diff -r 3233451a3bd6 -r c02720d1afee Gtf.pyc
Binary file Gtf.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Psl.py
--- a/Psl.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Psl.py	Fri Sep 30 15:14:24 2016 -0400
@@ -17,6 +17,8 @@
         self.name_psl = data_psl["name"]
         self.priority = data_psl["order_index"]
         self.track_color = data_psl["track_color"]
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = data_psl["group_name"]
 
         # Temporary files
         unsorted_bed_formatted_psl_file = tempfile.NamedTemporaryFile(suffix='.psl')
@@ -52,6 +54,7 @@
                          track_type='bigPsl', visibility='dense',
                          priority=self.priority,
                          track_file=my_big_psl_file_path,
-                         track_color=self.track_color)
+                         track_color=self.track_color,
+                         group_name=self.group_name)
 
         print("- BigPsl %s created" % self.name_psl)
\ No newline at end of file
diff -r 3233451a3bd6 -r c02720d1afee Psl.pyc
Binary file Psl.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee Track.py
--- a/Track.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/Track.py	Fri Sep 30 15:14:24 2016 -0400
@@ -1,6 +1,6 @@
 #!/usr/bin/python
 
-
+# TODO: Is this still useful?
 class Track(object):
     """Class to manage the track informations needed for Track Hub, in the TrackDb text file"""
 
diff -r 3233451a3bd6 -r c02720d1afee Track.pyc
Binary file Track.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee TrackDb.py
--- a/TrackDb.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/TrackDb.py	Fri Sep 30 15:14:24 2016 -0400
@@ -4,7 +4,7 @@
     """docstring for TrackDb"""
 
     def __init__(self, trackName="", longLabel="", shortLabel="", trackDataURL="", trackType="", visibility="",
-                 thickDrawItem='off', priority="0", track_color="#000000"):
+                 thickDrawItem='off', priority="0", track_color="#000000", group_name="Default"):
         super(TrackDb, self).__init__()
 
         self.trackName = trackName
@@ -16,3 +16,4 @@
         self.thickDrawItem = thickDrawItem
         self.priority = priority
         self.track_color = track_color
+        self.group_name = group_name
diff -r 3233451a3bd6 -r c02720d1afee TrackDb.pyc
Binary file TrackDb.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee TrackHub.py
--- a/TrackHub.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/TrackHub.py	Fri Sep 30 15:14:24 2016 -0400
@@ -33,11 +33,23 @@
         self.default_pos = None
         self.user_email = user_email
 
+        # Set containing the groups already added. Updated by addGroup()
+        self.groups = set()
+
         # TODO: Modify according to the files passed in parameter
+        # ---- Templates ----
+        # Template trackDb
         mylookup = TemplateLookup(directories=[os.path.join(tool_directory, 'templates/trackDb')],
                                   output_encoding='utf-8', encoding_errors='replace')
         self.trackDbTemplate = mylookup.get_template("layout.txt")
 
+        # Template groups
+        mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates/groupsTxt')],
+                                  output_encoding='utf-8', encoding_errors='replace')
+        self.groupsTemplate = mylookup.get_template("layout.txt")
+
+        # ---- End Templates ----
+
         self.extra_files_path = extra_files_path
         self.outputFile = outputFile
 
@@ -68,16 +80,43 @@
     def addTrack(self, trackDbObject=None):
         # Create the trackDb.txt file in the specie folder, if not exists
         # Else append the new track
+        # TODO: Get this out of the function
         trackDbTxtFilePath = os.path.join(self.mySpecieFolderPath, 'trackDb.txt')
 
         # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
         with open(trackDbTxtFilePath, 'a+') as trackDbFile:
             trackDbs = [trackDbObject]
+
+            # TODO: The addGroup does not belong here. Move it when the group becomes more than just a label
+            # Add the group as well, if exists in trackDbObject
+            self.addGroup(trackDbObject.group_name)
+
             htmlMakoRendered = self.trackDbTemplate.render(
                 trackDbs=trackDbs
             )
             trackDbFile.write(htmlMakoRendered)
 
+    def addGroup(self, group_name="Default"):
+        # If not already present in self.groups, add to groups.txt
+        # Create the trackDb.txt file in the specie folder, if not exists
+        # Else append the new track
+        # TODO: Get this out of the function
+        groupsTxtFilePath = os.path.join(self.mySpecieFolderPath, 'groups.txt')
+
+        # If the group is already present, we don't need to add it
+        if group_name in self.groups:
+            return
+
+        # Append to trackDbTxtFilePath the trackDbTemplate populate with the newTrack object
+        with open(groupsTxtFilePath, 'a+') as groupFile:
+            # Add the group as well, if exists in trackDbObject
+
+            htmlMakoRendered = self.groupsTemplate.render(
+                    label=group_name
+            )
+            groupFile.write(htmlMakoRendered)
+        self.groups.add(group_name)
+
     def terminate(self):
         # Just a test to output a simple HTML
         # TODO: Create a class to handle the file object
@@ -182,8 +221,8 @@
 
         # Create the file groups.txt
         # TODO: If not inputs for this, do no create the file
-        groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
-        self.__fillGroupsTxtFile__(groupsTxtFilePath)
+        # groupsTxtFilePath = os.path.join(mySpecieFolderPath, 'groups.txt')
+        # self.__fillGroupsTxtFile__(groupsTxtFilePath)
 
         # Create the folder tracks into the specie folder
         tracksFolderPath = os.path.join(mySpecieFolderPath, "tracks")
diff -r 3233451a3bd6 -r c02720d1afee TrackHub.pyc
Binary file TrackHub.pyc has changed
diff -r 3233451a3bd6 -r c02720d1afee hubArchiveCreator.py
--- a/hubArchiveCreator.py	Sun Sep 25 11:25:38 2016 -0400
+++ b/hubArchiveCreator.py	Fri Sep 30 15:14:24 2016 -0400
@@ -126,7 +126,6 @@
     # We remove the spaces in ["name"] of inputs_data
     sanitize_name_inputs(inputs_data)
 
-
     # TODO: Check here all the binaries / tools we need. Exception if missing
 
     # Create the Track Hub folder
diff -r 3233451a3bd6 -r c02720d1afee hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Sun Sep 25 11:25:38 2016 -0400
+++ b/hubArchiveCreator.xml	Fri Sep 30 15:14:24 2016 -0400
@@ -12,7 +12,8 @@
         <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
         <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
         <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
-        <requirement type="package" version="332">ucsc-psltobigpsl</requirement>
+        <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
+        <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
         <requirement type="package" version="332">ucsc-twobitinfo</requirement>
         <requirement type="package" version="1.3">samtools</requirement>
         <!-- ToolShed dependencies -->
@@ -21,6 +22,7 @@
         <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
         <requirement type="package" version="0.0.1">genePredToBed</requirement>
         <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
+        <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
     </requirements>
 
@@ -60,48 +62,59 @@
 
         #end def
 
-        #for $i, $f in enumerate( $format )
-            #set track_color = str($f.formatChoice.track_color)
+        #for $i_g, $g in enumerate( $group )
+            #for $i, $f in enumerate( $g.format )
+
+                ## For each format, we have a few mandatory fields we store in a dict
+                #set track_color = str($f.formatChoice.track_color)
+                #set group_name = str($g.group_name)
 
-            #if $f.formatChoice.format_select == "bam"
-                --bam $f.formatChoice.BAM
-                #set bam_index = $f.formatChoice.BAM.metadata.bam_index
-                #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index,
-                                                                "track_color": $track_color})
-            #end if
-            #if $f.formatChoice.format_select == "bed"
-                #if $f.formatChoice.bedChoice.bed_select == "bed"
-                    --bed $f.formatChoice.bedChoice.BED
-                    #silent $prepare_json($f.formatChoice.bedChoice.BED, $i,
-                                            {"track_color": $track_color})
-                #end if
-                #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
-                    --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
-                    #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i,
-                                            {"track_color": $track_color})
+                #set extra_data_dict = {"track_color": $track_color,
+                                        "group_name": $group_name}
+
+                #if $f.formatChoice.format_select == "bam"
+                    --bam $f.formatChoice.BAM
+                    #set bam_index = $f.formatChoice.BAM.metadata.bam_index
+
+                    ## Add Bam format specific fields
+                    #silent extra_data_dict.update({"index": $bam_index})
+
+                    #silent $prepare_json($f.formatChoice.BAM, $i, extra_data_dict)
                 #end if
-            #end if
-            #if $f.formatChoice.format_select == "psl"
-                --psl $f.formatChoice.PSL
-                #silent $prepare_json($f.formatChoice.PSL, $i,
-                                        {"track_color": $track_color})
-            #end if
-            #if $f.formatChoice.format_select == "bigwig"
-                --bigwig $f.formatChoice.BIGWIG
-                #silent $prepare_json($f.formatChoice.BIGWIG, $i,
-                                        {"track_color": $track_color})
-            #end if
-            #if $f.formatChoice.format_select == "gff3"
-                --gff3 $f.formatChoice.GFF3
-                #silent $prepare_json($f.formatChoice.GFF3, $i,
-                                        {"track_color": $track_color})
-            #end if
-            #if $f.formatChoice.format_select == "gtf"
-                ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
-                --gtf $f.formatChoice.GTF
-                #silent $prepare_json($f.formatChoice.GTF, $i,
-                                         {"track_color": $track_color})
-            #end if
+                #if $f.formatChoice.format_select == "bed"
+                    #if $f.formatChoice.bedChoice.bed_select == "bed"
+                        --bed $f.formatChoice.bedChoice.BED
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED, $i,
+                                                extra_data_dict)
+                    #end if
+                    #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
+                        --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
+                        #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i,
+                                                extra_data_dict)
+                    #end if
+                #end if
+                #if $f.formatChoice.format_select == "psl"
+                    --psl $f.formatChoice.PSL
+                    #silent $prepare_json($f.formatChoice.PSL, $i,
+                                           extra_data_dict)
+                #end if
+                #if $f.formatChoice.format_select == "bigwig"
+                    --bigwig $f.formatChoice.BIGWIG
+                    #silent $prepare_json($f.formatChoice.BIGWIG, $i,
+                                            extra_data_dict)
+                #end if
+                #if $f.formatChoice.format_select == "gff3"
+                    --gff3 $f.formatChoice.GFF3
+                    #silent $prepare_json($f.formatChoice.GFF3, $i,
+                                            extra_data_dict)
+                #end if
+                #if $f.formatChoice.format_select == "gtf"
+                    ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
+                    --gtf $f.formatChoice.GTF
+                    #silent $prepare_json($f.formatChoice.GTF, $i,
+                                             extra_data_dict)
+                #end if
+            #end for
         #end for
 
         ## We combine the fasta file dataset name with his false path in a JSON object
@@ -139,126 +152,129 @@
                 type="data"
                 label="Reference genome"
         />
-        <repeat name="format" title="Formats">
-            <conditional name="formatChoice">
-                <param name="format_select" type="select" label="Format">
-                    <option value="bam" selected="true">BAM</option>
-                    <option value="bed">BED</option>
-                    <option value="psl">PSL</option>
-                    <option value="bigwig">BIGWIG</option>
-                    <option value="gff3">GFF3</option>
-                    <option value="gtf">GTF</option>
-                </param>
-
-                <when value="bam">
-                    <param
-                            format="bam"
-                            name="BAM"
-                            type="data"
-                            label="BAM File"
-                    />
-                    <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
-                    <param name="track_color" type="color" label="Track color" value="#000000">
-                        <sanitizer>
-                            <valid initial="string.letters,string.digits">
-                                <add value="#"/>
-                            </valid>
-                        </sanitizer>
-                    </param>
-                </when>
-                <when value="bed">
-                    <conditional name="bedChoice">
-                        <param name="bed_select" type="select" label="Bed Choice">
-                            <option value="bed" selected="true">BED Generic (bed3+)</option>
-                            <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
-                        </param>
-                        <when value="bed">
-                            <param
-                                    format="bed"
-                                    name="BED"
-                                    type="data"
-                                    label="Generic Bed File Choice"
-                            />
-
-                        </when>
-                        <when value="bed_simple_repeats_option">
-                            <param
-                                    format="bed"
-                                    name="BED_simple_repeats"
-                                    type="data"
-                                    label="Bed Simple Repeats (Bed4+12) File"
-                            />
-                        </when>
-                    </conditional>
-                    <param name="track_color" type="color" label="Track color" value="#000000">
-                        <sanitizer>
-                            <valid initial="string.letters,string.digits">
-                                <add value="#"/>
-                            </valid>
-                        </sanitizer>
+        <repeat name="group" title="New group">
+            <param type="text" name="group_name" label="Group name" value="Default group"/>
+            <repeat name="format" title="New track">
+                <conditional name="formatChoice">
+                    <param name="format_select" type="select" label="Format">
+                        <option value="bam" selected="true">BAM</option>
+                        <option value="bed">BED</option>
+                        <option value="psl">PSL</option>
+                        <option value="bigwig">BIGWIG</option>
+                        <option value="gff3">GFF3</option>
+                        <option value="gtf">GTF</option>
                     </param>
-                </when>
-                <when value="psl">
-                    <param
-                            format="psl"
-                            name="PSL"
-                            type="data"
-                            label="PSL 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>
-                <when value="bigwig">
-                    <param
-                            format="bigwig"
-                            name="BIGWIG"
-                            type="data"
-                            label="BIGWIG 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>
-                <when value="gff3">
-                    <param
-                            format="gff3"
-                            name="GFF3"
-                            type="data"
-                            label="GFF3 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>
-                <when value="gtf">
-                    <param
-                            format="gtf"
-                            name="GTF"
-                            type="data"
-                            label="GTF 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>
+
+                    <when value="bam">
+                        <param
+                                format="bam"
+                                name="BAM"
+                                type="data"
+                                label="BAM File"
+                        />
+                        <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>
+                    <when value="bed">
+                        <conditional name="bedChoice">
+                            <param name="bed_select" type="select" label="Bed Choice">
+                                <option value="bed" selected="true">BED Generic (bed3+)</option>
+                                <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
+                            </param>
+                            <when value="bed">
+                                <param
+                                        format="bed"
+                                        name="BED"
+                                        type="data"
+                                        label="Generic Bed File Choice"
+                                />
+
+                            </when>
+                            <when value="bed_simple_repeats_option">
+                                <param
+                                        format="bed"
+                                        name="BED_simple_repeats"
+                                        type="data"
+                                        label="Bed Simple Repeats (Bed4+12) File"
+                                />
+                            </when>
+                        </conditional>
+                        <param name="track_color" type="color" label="Track color" value="#000000">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                    <add value="#"/>
+                                </valid>
+                            </sanitizer>
+                        </param>
+                    </when>
+                    <when value="psl">
+                        <param
+                                format="psl"
+                                name="PSL"
+                                type="data"
+                                label="PSL 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>
+                    <when value="bigwig">
+                        <param
+                                format="bigwig"
+                                name="BIGWIG"
+                                type="data"
+                                label="BIGWIG 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>
+                    <when value="gff3">
+                        <param
+                                format="gff3"
+                                name="GFF3"
+                                type="data"
+                                label="GFF3 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>
+                    <when value="gtf">
+                        <param
+                                format="gtf"
+                                name="GTF"
+                                type="data"
+                                label="GTF 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>
         <conditional name="advanced_options">
             <param name="advanced_options_selector" type="select" label="Advanced options">
diff -r 3233451a3bd6 -r c02720d1afee templates/groupsTxt/layout.txt
--- a/templates/groupsTxt/layout.txt	Sun Sep 25 11:25:38 2016 -0400
+++ b/templates/groupsTxt/layout.txt	Fri Sep 30 15:14:24 2016 -0400
@@ -1,4 +1,5 @@
-name ${mapName}
-label ${labelMapping}
-priority ${prioriy}
-defaultIsClosed ${isClosed}
+name ${label.lower().replace(' ', '_')}
+label ${label}
+priority 2
+defaultIsClosed 0
+
diff -r 3233451a3bd6 -r c02720d1afee templates/trackDb/layout.txt
--- a/templates/trackDb/layout.txt	Sun Sep 25 11:25:38 2016 -0400
+++ b/templates/trackDb/layout.txt	Fri Sep 30 15:14:24 2016 -0400
@@ -9,5 +9,6 @@
     thickDrawItem ${trackDb.thickDrawItem}
     priority ${trackDb.priority}
     color ${trackDb.track_color}
+    group ${trackDb.group_name.lower().replace(' ', '_')}
 
 % endfor
diff -r 3233451a3bd6 -r c02720d1afee tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Sep 25 11:25:38 2016 -0400
+++ b/tool_dependencies.xml	Fri Sep 30 15:14:24 2016 -0400
@@ -105,4 +105,27 @@
         </install>
         <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
     </package>
+
+    <!-- Package pslToBigPsl -->
+    <package name="pslToBigPsl" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action target_directory="bin" type="download_binary">
+                    <url_template os="darwin">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl
+                    </url_template>
+                    <url_template os="linux">
+                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl
+                    </url_template>
+                </action>
+                <action type="chmod">
+                    <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
+    </package>
 </tool_dependency>