# HG changeset patch
# User yating-l
# Date 1529445591 14400
# Node ID 43a700afd45734ab524dab27c26e214e9306c2cc
# Parent  9161beae834fb4193288ea49a19ccb1c1752c996
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187

diff -r 9161beae834f -r 43a700afd457 README.md
--- a/README.md	Sat Jun 02 13:08:46 2018 -0400
+++ b/README.md	Tue Jun 19 17:59:51 2018 -0400
@@ -1,5 +1,5 @@
 # JBrowse Hub Creator
-This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
+This Galaxy tool is used to prepare your files to be ready for JBrowse visualization.
 
 ## Features
 1. Similar interface to Hub Archive Creator.
@@ -7,33 +7,36 @@
 3. Group the tracks 
 4. Set the color for each track
 5. Set the label for each track
-6. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
+6. Support generating Tabix Indexed CanVasFeatures tracks
+7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
 
 At the moment, Supported datatypes are:
-- Bam
-- Bed 
+- BAM
+- BED
+  - Generic BED
   - Splice Junctions (BED 12+1)
   - Simple Repeats (BED 4+12)
+  - BLAT alignment (BigPsl)
+  - BLAST alignment (BED 12+12)
 - BigWig
-- Gff3
-- Gtf
-- Blastxml
-- BigPsl
+- GFF3
+- GTF
+- Blast XML output
 
 ## Installation:
-1. You would need to add this tool into your Galaxy.
-  1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7)
-  2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
-2. The tool can be used with or without Conda (activate it in your galaxy.ini)
-3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy.
-   You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits)
+
+**ToolShed Installation**: 
 
+- The JBrowse Archive Creator tool is published at [ToolShed Repository](https://toolshed.g2.bx.psu.edu/view/yating-l/jbrowsearchivecreator)
+
+- Refer to [Installing Tools into Galaxy](https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial) tutorial if you want to learn how to install a tool from ToolShed.
+  
 ## Future
 See [TODO.md](todo.md) for more information
 
 ## Contribute
 
-- Source Code: https://github.com/Yating-L/jbrowse_hub
+- Source Code: https://github.com/goeckslab/jbrowse-archive-creator.git
 
 ## Support
 
@@ -41,7 +44,7 @@
 
 - For more information about how to use G-OnRamp:
     - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
-    - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer
+    - [Yating Liu](yliu41@wustl.edu) - Community manager and developer
 
 - For more information about the project vision, or for partneship:
     - [Elgin, Sarah](selgin@wustl.edu) - PI
diff -r 9161beae834f -r 43a700afd457 TrackHub.py
--- a/TrackHub.py	Sat Jun 02 13:08:46 2018 -0400
+++ b/TrackHub.py	Tue Jun 19 17:59:51 2018 -0400
@@ -51,10 +51,12 @@
         if Datatype.trackType == 'HTMLFeatures':
             self.myTrackStyle = TrackStyles(self.tool_directory, self.mySpecieFolderPath, self.trackList)
         self.logger = logging.getLogger(__name__)
+        self.nameIndexTrackList = []
 
-    
 
     def addTrack(self, trackDbObject):
+        if trackDbObject['nameIndex'] == "true":
+            self.nameIndexTrackList.append(trackDbObject['trackLabel'])
         if trackDbObject['dataType'].lower() == 'bam':
             subtools.add_track_json(self.trackList, trackDbObject['options'])
         elif trackDbObject['dataType'].lower() == 'bigwig':
@@ -104,8 +106,9 @@
         subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
 
     def _indexName(self):
-        subtools.generate_names(self.mySpecieFolderPath)
-        print "finished name index \n"
+        if self.nameIndexTrackList:
+            subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
+            print "finished name index \n"
 
     def _outHtml(self):
         mylookup = TemplateLookup(directories=[os.path.join(self.tool_directory, 'templates')],
diff -r 9161beae834f -r 43a700afd457 datatypes/Datatype.py
--- a/datatypes/Datatype.py	Sat Jun 02 13:08:46 2018 -0400
+++ b/datatypes/Datatype.py	Tue Jun 19 17:59:51 2018 -0400
@@ -98,6 +98,8 @@
             self.extraSettings["category"] = self.trackSettings["group_name"]
         if "track_color" in self.trackSettings and self.trackSettings["track_color"]:
             self.extraSettings["color"] = self.trackSettings["track_color"]
+        #store information of whether to generate name index for the track
+        self.extraSettings["nameIndex"] = self.trackSettings["nameIndex"]
         
         
     @abc.abstractmethod
diff -r 9161beae834f -r 43a700afd457 datatypes/Datatype.pyc
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diff -r 9161beae834f -r 43a700afd457 datatypes/converters/DataConversion.pyc
Binary file datatypes/converters/DataConversion.pyc has changed
diff -r 9161beae834f -r 43a700afd457 datatypes/converters/bedToGff3.pyc
Binary file datatypes/converters/bedToGff3.pyc has changed
diff -r 9161beae834f -r 43a700afd457 datatypes/converters/blastxmlToGff3.pyc
Binary file datatypes/converters/blastxmlToGff3.pyc has changed
diff -r 9161beae834f -r 43a700afd457 datatypes/interval/Bed.pyc
Binary file datatypes/interval/Bed.pyc has changed
diff -r 9161beae834f -r 43a700afd457 datatypes/interval/Interval.pyc
Binary file datatypes/interval/Interval.pyc has changed
diff -r 9161beae834f -r 43a700afd457 datatypes/interval/__init__.pyc
Binary file datatypes/interval/__init__.pyc has changed
diff -r 9161beae834f -r 43a700afd457 jbrowse-archive-creator.iml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse-archive-creator.iml	Tue Jun 19 17:59:51 2018 -0400
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff -r 9161beae834f -r 43a700afd457 jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Sat Jun 02 13:08:46 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Tue Jun 19 17:59:51 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.5">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.2.1">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
@@ -81,6 +81,7 @@
         #set track_color = str($f.formatChoice.track_color)
         #set group_name = str($g.group_name)
         #set longLabel = str($f.formatChoice.longLabel)
+
         #set extra_data_dict = {"track_color": $track_color,
                                 "group_name": $group_name,
                                 "long_label": $longLabel}
@@ -88,11 +89,12 @@
             #set bam_index = $f.formatChoice.BAM.metadata.bam_index
 
             ## Add Bam format specific fields
-            #silent $extra_data_dict.update({"index": $bam_index})
+            #silent $extra_data_dict.update({"index": $bam_index, "nameIndex": str($f.formatChoice.nameIndex)})
 
             #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
         #end if
         #if $f.formatChoice.format_select == "bed"
+            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.bedChoice.nameIndex)})
             #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
                 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
                                                 $extra_data_dict)
@@ -119,18 +121,22 @@
             #end if
         #end if
         #if $f.formatChoice.format_select == "blastxml"
-                #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, 
+            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
+            #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
                                             extra_data_dict)
         #end if
         #if $f.formatChoice.format_select == "bigwig"
+            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
             #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
                                             $extra_data_dict)
         #end if
         #if $f.formatChoice.format_select == 'gff3'
+            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
             #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
                                             $extra_data_dict)
         #end if
         #if $f.formatChoice.format_select == "gtf"
+            #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
             ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
             #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
                                              $extra_data_dict)
@@ -200,11 +206,12 @@
                                 </valid>
                             </sanitizer>
                         </param>
+                        <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                     </when>     
                     <when value="bed">
                         <conditional name="bedChoice">
                             <param name="bed_select" type="select" label="Bed Choice">
-                                <option value="bed_generic">BED format</option>
+                                <option value="bed_generic">BED Generic</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="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
@@ -217,6 +224,7 @@
                                         type="data"
                                         label="Bed File"
                                 />
+                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                             </when>
                             <when value="bed_simple_repeats_option">
                                 <param
@@ -225,6 +233,7 @@
                                         type="data"
                                         label="Bed Simple Repeats (Bed4+12) File"
                                 />
+                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                             </when>
                             <when value="bed_splice_junctions_option">
                                 <param
@@ -233,6 +242,7 @@
                                         type="data"
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
+                                <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                             </when>
                             <when value="bed_blast_alignment_option">
                                 <param
@@ -241,6 +251,7 @@
                                         type="data"
                                         label="Bed Blast Alignments (Bed12+12) File"
                                 />
+                                <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                             </when>
                             <when value="bed_blat_alignment_option">
                                 <param
@@ -249,6 +260,7 @@
                                         type="data"
                                         label="Bed BLAT Alignments (bigPsl) File"
                                 />
+                                <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                             </when>
                         </conditional>
                         <param name="longLabel" type="text" size="30" label="Track label" />
@@ -275,6 +287,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
+                        <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                     </when>
                     <when value="bigwig">
                         <param
@@ -291,6 +304,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
+                        <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                     </when>
                     <when value="gff3">
                         <param
@@ -307,6 +321,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
+                        <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                     </when>
                     <when value="gtf">
                         <param
@@ -323,7 +338,8 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                    </when>  
+                        <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                    </when>
                 </conditional>
             </repeat>
         </repeat>
diff -r 9161beae834f -r 43a700afd457 tracks/BamFeatures.pyc
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diff -r 9161beae834f -r 43a700afd457 tracks/BigwigFeatures.pyc
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diff -r 9161beae834f -r 43a700afd457 tracks/CanvasFeatures.pyc
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diff -r 9161beae834f -r 43a700afd457 tracks/HTMLFeatures.pyc
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diff -r 9161beae834f -r 43a700afd457 tracks/TrackDb.py
--- a/tracks/TrackDb.py	Sat Jun 02 13:08:46 2018 -0400
+++ b/tracks/TrackDb.py	Tue Jun 19 17:59:51 2018 -0400
@@ -40,7 +40,8 @@
                 ("dataType", self.dataType),
                 ("trackType", self.trackType)]
                 )
-        
+
+        self.track_db["nameIndex"] = self.extraSettings['nameIndex']
         
         extraConfigs = self.prepareExtraSetting()
         self.logger.debug("Generate extraConfigs = %s", json.dumps(extraConfigs))
diff -r 9161beae834f -r 43a700afd457 tracks/TrackDb.pyc
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diff -r 9161beae834f -r 43a700afd457 tracks/__init__.pyc
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diff -r 9161beae834f -r 43a700afd457 util/Reader.py
--- a/util/Reader.py	Sat Jun 02 13:08:46 2018 -0400
+++ b/util/Reader.py	Tue Jun 19 17:59:51 2018 -0400
@@ -120,11 +120,15 @@
         # TODO: Optimize this double loop
         for input_data in array_inputs:
             input_false_path = input_data["false_path"]
-            input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
-            extensionObject = ExtensionClass(input_false_path, input_data)
-            extensionObject.generateCustomTrack()
-            datatype_dictionary.update({input_data["order_index"]: extensionObject})
-            self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
+            # if the file is empty, skip the rest
+            if os.path.isfile(input_false_path) and os.path.getsize(input_false_path) > 0:
+                input_data["name"] = santitizer.sanitize_name_input(input_data["name"])
+                extensionObject = ExtensionClass(input_false_path, input_data)
+                extensionObject.generateCustomTrack()
+                datatype_dictionary.update({input_data["order_index"]: extensionObject})
+                self.logger.debug("%s object: %s has been created", ExtensionClass, input_data["name"])
+            else:
+                self.logger.info("The input file: %s is empty, skip creating the track for this data", input_data["name"])
         return datatype_dictionary
 
     
diff -r 9161beae834f -r 43a700afd457 util/santitizer.pyc
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diff -r 9161beae834f -r 43a700afd457 util/subtools.py
--- a/util/subtools.py	Sat Jun 02 13:08:46 2018 -0400
+++ b/util/subtools.py	Tue Jun 19 17:59:51 2018 -0400
@@ -382,8 +382,10 @@
     p = _handleExceptionAndCheckCall(array_call)
     return p       
 
-def generate_names(outputFolder, hashBits=4):
-    array_call = ['generate-names.pl', '--hashBits', '4', '-v', '--out', outputFolder]
+def generate_names(outputFolder, nameIndexTrackList, hashBits=4):
+    array_call = ['generate-names.pl', '--hashBits', str(hashBits), '-v', '--completionLimit', '0', '--out', outputFolder]
+    array_call.append('--tracks')
+    array_call.append(','.join(nameIndexTrackList))
     p = _handleExceptionAndCheckCall(array_call)
     return p  
    
diff -r 9161beae834f -r 43a700afd457 util/subtools.pyc
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