# HG changeset patch
# User yating-l
# Date 1529444352 14400
# Node ID 1eb4adefd7472c99d900cdc79fd2a7ae9642ad69
# Parent  061da5d3a219a9c9ca37d221474ff9e9013a88c2
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 97a743ee6d228c8a0a5778ec3cb6f68a2e22c8e3

diff -r 061da5d3a219 -r 1eb4adefd747 TrackHub.py
--- a/TrackHub.py	Tue Jun 19 16:28:36 2018 -0400
+++ b/TrackHub.py	Tue Jun 19 17:39:12 2018 -0400
@@ -56,7 +56,7 @@
 
     def addTrack(self, trackDbObject):
         if trackDbObject['nameIndex'] == "true":
-            self.nameIndexTracksList.append(trackDbObject['trackLabel'])
+            self.nameIndexTrackList.append(trackDbObject['trackLabel'])
         if trackDbObject['dataType'].lower() == 'bam':
             subtools.add_track_json(self.trackList, trackDbObject['options'])
         elif trackDbObject['dataType'].lower() == 'bigwig':
@@ -106,8 +106,9 @@
         subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
 
     def _indexName(self):
-        subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
-        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 061da5d3a219 -r 1eb4adefd747 datatypes/Datatype.py
--- a/datatypes/Datatype.py	Tue Jun 19 16:28:36 2018 -0400
+++ b/datatypes/Datatype.py	Tue Jun 19 17:39:12 2018 -0400
@@ -49,7 +49,6 @@
         self.track = None
         self.trackSettings = dict()
         self.extraSettings = collections.OrderedDict()
-        self.nameIndex = False
         
 
     @staticmethod
diff -r 061da5d3a219 -r 1eb4adefd747 jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Tue Jun 19 16:28:36 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Tue Jun 19 17:39:12 2018 -0400
@@ -206,7 +206,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                        <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                        <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">
@@ -224,7 +224,7 @@
                                         type="data"
                                         label="Bed File"
                                 />
-                                <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                                <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
@@ -233,7 +233,7 @@
                                         type="data"
                                         label="Bed Simple Repeats (Bed4+12) File"
                                 />
-                                <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                                <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
@@ -242,7 +242,7 @@
                                         type="data"
                                         label="Bed Splice Junctions (Bed12+1) File"
                                 />
-                                <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                                <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
@@ -251,7 +251,7 @@
                                         type="data"
                                         label="Bed Blast Alignments (Bed12+12) File"
                                 />
-                                <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                                <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
@@ -260,7 +260,7 @@
                                         type="data"
                                         label="Bed BLAT Alignments (bigPsl) File"
                                 />
-                                <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                                <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" />
@@ -287,7 +287,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                        <param name="nameIndex" type="boolean" value="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                        <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
@@ -304,7 +304,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                        <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                        <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
@@ -321,7 +321,7 @@
                                 </valid>
                             </sanitizer>
                         </param>
-                        <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
+                        <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
@@ -337,8 +337,8 @@
                                     <add value="#"/>
                                 </valid>
                             </sanitizer>
-                            <param name="nameIndex" type="boolean" value="false" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
                         </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>
                 </conditional>
             </repeat>
diff -r 061da5d3a219 -r 1eb4adefd747 util/subtools.py
--- a/util/subtools.py	Tue Jun 19 16:28:36 2018 -0400
+++ b/util/subtools.py	Tue Jun 19 17:39:12 2018 -0400
@@ -383,10 +383,9 @@
     return p       
 
 def generate_names(outputFolder, nameIndexTrackList, hashBits=4):
-    array_call = ['generate-names.pl', '--hashBits', hashBits, '-v', '--completionLimit', '0', '--out', outputFolder]
-    if nameIndexTrackList:
-        array_call.append('--tracks')
-        array_call.append(','.join(nameIndexTrackList))
+    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