Mercurial > repos > rmarenco > hubarchivecreator

changeset 28:6aa28a85cc38 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5bbecd016ad3a784ad030cb82a09a3ac40dc6060
author yating-l
date Mon, 10 Jul 2017 17:08:38 -0400
parents cdd33c5c8ac1
children 7e8a8b732db3
files Bed.py cytoBand.py hubArchiveCreator.xml
diffstat 3 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/Bed.py	Mon Jul 10 12:28:50 2017 -0400
+++ b/Bed.py	Mon Jul 10 17:08:38 2017 -0400
@@ -44,6 +44,8 @@
             subtools.bedToBigBed(self.sortedBedFile.name,
                                  self.chromSizesFile.name,
                                  self.bigBedFile.name,
+                                 typeOption='bed4',
+                                 tab='True',
                                  extraIndex='name'
                                  )
 
--- a/cytoBand.py	Mon Jul 10 12:28:50 2017 -0400
+++ b/cytoBand.py	Mon Jul 10 17:08:38 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
--- a/hubArchiveCreator.xml	Mon Jul 10 12:28:50 2017 -0400
+++ b/hubArchiveCreator.xml	Mon Jul 10 17:08:38 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.1">
+<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>