# HG changeset patch
# User yating-l
# Date 1499720771 14400
# Node ID 4c4e8941fedafce0410ed8dba57447bece4ceb0f
# Parent  68aeb6482069f6f27072abdd7280ed36771a0aa5
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060-dirty

diff -r 68aeb6482069 -r 4c4e8941feda Bed.py
--- a/Bed.py	Mon Jul 03 17:24:49 2017 -0400
+++ b/Bed.py	Mon Jul 10 17:06:11 2017 -0400
@@ -44,6 +44,8 @@
             subtools.bedToBigBed(self.sortedBedFile.name,
                                  self.chromSizesFile.name,
                                  self.bigBedFile.name,
+                                 typeOption='bed4',
+                                 tab='True',
                                  extraIndex='name'
                                  )
 
diff -r 68aeb6482069 -r 4c4e8941feda cytoBand.py
--- a/cytoBand.py	Mon Jul 03 17:24:49 2017 -0400
+++ b/cytoBand.py	Mon Jul 10 17:06:11 2017 -0400
@@ -41,7 +41,8 @@
             subtools.bedToBigBed(sortedBedFile.name,
                                  self.chromSizesFile.name,
                                  bigBedFile.name,
-                                 typeOption='bed4',
+                                 typeOption='bed4+1',
+                                 tab='True',
                                  autoSql=auto_sql_option)
 
         # Create the Track Object
diff -r 68aeb6482069 -r 4c4e8941feda hubArchiveCreator.xml
--- a/hubArchiveCreator.xml	Mon Jul 03 17:24:49 2017 -0400
+++ b/hubArchiveCreator.xml	Mon Jul 10 17:06:11 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
+<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2">
     <description>
         This Galaxy tool permits to prepare your files to be ready for
         Assembly Hub visualization.
@@ -222,8 +222,8 @@
                     <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_cytoBand">cytoBand Track (bed4)</option>
+                                <option value="bed_generic" selected="true">BED Generic (bed4)</option>
+                                <option value="bed_cytoBand">cytoBand Track (bed4+1)</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>
diff -r 68aeb6482069 -r 4c4e8941feda templates/trackDb/layout.txt
--- a/templates/trackDb/layout.txt	Mon Jul 03 17:24:49 2017 -0400
+++ b/templates/trackDb/layout.txt	Mon Jul 10 17:06:11 2017 -0400
@@ -30,15 +30,23 @@
         % if "NCBI" in trackDb.database:
 url https://www.ncbi.nlm.nih.gov/protein/$$
 urlLabel ${trackDb.database} Details:
+iframeUrl https://www.ncbi.nlm.nih.gov/protein/$$
+iframeOptions height='600' width='800'
         % elif "UniProt" in trackDb.database:
 url http://www.uniprot.org/uniprot/$$
 urlLabel ${trackDb.database} Details:
+iframeUrl http://www.uniprot.org/uniprot/$$
+iframeOptions height='600' width='800'
         % elif "FlyBase" in trackDb.database:
 url http://flybase.org/reports/$$
 urlLabel ${trackDb.database} Details:
+iframeUrl http://flybase.org/reports/$$
+iframeOptions height='600' width='800'
         % else:
 url https://www.ncbi.nlm.nih.gov/gquery/?term=$$
 urlLabel NCBI Details:
+iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$
+iframeOptions height='600' width='800'
         % endif
         
     % elif "bigPsl" in trackDb.trackType and trackDb.database:
@@ -57,9 +65,13 @@
     % if "NCBI" in trackDb.database:
 url https://www.ncbi.nlm.nih.gov/nuccore/$$
 urlLabel NCBI Details:
+iframeUrl https://www.ncbi.nlm.nih.gov/nuccore/$$
+iframeOptions height='600' width='800'
     % else:
 url https://www.ncbi.nlm.nih.gov/gquery/?term=$$
 urlLabel NCBI Details:
+iframeUrl https://www.ncbi.nlm.nih.gov/gquery/?term=$$
+iframeOptions height='600' width='800'
     % endif
 
     % else: