# HG changeset patch
# User yating-l
# Date 1532101081 14400
# Node ID 804e7217f27c553bdd82d68b6ecea1ed510c7369
# Parent  be34d213ec6aee01a8afacfddb8ca780a11c1772
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty

diff -r be34d213ec6a -r 804e7217f27c TrackHub.py
--- a/TrackHub.py	Wed Jun 20 17:23:48 2018 -0400
+++ b/TrackHub.py	Fri Jul 20 11:38:01 2018 -0400
@@ -106,9 +106,8 @@
         subtools.prepare_refseqs(self.reference_genome.false_path, self.mySpecieFolderPath)
 
     def _indexName(self):
-        if self.nameIndexTrackList:
-            subtools.generate_names(self.mySpecieFolderPath, self.nameIndexTrackList)
-            print "finished name index \n"
+        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 be34d213ec6a -r 804e7217f27c jbrowseArchiveCreator.xml
--- a/jbrowseArchiveCreator.xml	Wed Jun 20 17:23:48 2018 -0400
+++ b/jbrowseArchiveCreator.xml	Fri Jul 20 11:38:01 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0">
+<tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2">
     <description>
         This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
     </description>
@@ -199,6 +199,7 @@
                                 type="data"
                                 label="BAM 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" />
                         <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -207,7 +208,6 @@
                                 </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">
@@ -296,6 +296,7 @@
                             <option value="FlyBase">FlyBase</option>
                             <option value="Others">Others</option>
                         </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" />
                         <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -304,7 +305,6 @@
                                 </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
@@ -313,6 +313,7 @@
                                 type="data"
                                 label="BIGWIG 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" />
                         <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -321,7 +322,6 @@
                                 </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
@@ -330,6 +330,7 @@
                             type="data"
                             label="GFF3 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" />
                         <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -338,7 +339,6 @@
                                 </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
@@ -347,6 +347,7 @@
                                 type="data"
                                 label="GTF 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" />
                         <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
                         <param name="track_color" type="color" label="Track color" value="#000000">
                             <sanitizer>
@@ -355,7 +356,6 @@
                                 </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>
                 </conditional>
             </repeat>
diff -r be34d213ec6a -r 804e7217f27c util/subtools.py
--- a/util/subtools.py	Wed Jun 20 17:23:48 2018 -0400
+++ b/util/subtools.py	Fri Jul 20 11:38:01 2018 -0400
@@ -384,8 +384,9 @@
 
 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))
+    if nameIndexTrackList:
+        array_call.append('--tracks')
+        array_call.append(','.join(nameIndexTrackList))
     p = _handleExceptionAndCheckCall(array_call)
     return p