# HG changeset patch
# User yating-l
# Date 1489519247 14400
# Node ID 99d66676570b8494c0baaccb81315c5dca5151ad
# Parent  f2285f29a6fa58033832c4459f53f310a0dc56a5
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

diff -r f2285f29a6fa -r 99d66676570b jbrowse_hub.xml
--- a/jbrowse_hub.xml	Tue Mar 14 15:15:54 2017 -0400
+++ b/jbrowse_hub.xml	Tue Mar 14 15:20:47 2017 -0400
@@ -27,6 +27,9 @@
             #if $f.formatChoice.format_select == 'bam'
                 --bam $f.formatChoice.BAM
             #end if
+            #if $f.formatChoice.format_select == 'bai'
+                --bam $f.formatChoice.BAI
+            #end if
             #if $f.formatChoice.format_select == 'gff3_transcript'
                 --gff3_transcript $f.formatChoice.GFF3_transcript
             #end if
@@ -55,6 +58,7 @@
                 <conditional name="formatChoice">
                     <param name="format_select" type="select" label="Format">
                         <option value="bam" selected="true">BAM</option>
+                        <option value="bai" selected="true">BAI (BAM index)</option>
                         <option value="bed">BED</option>
                         <option value="blastxml">BLASTXML</option>
                         <option value="bigwig">BIGWIG</option>
@@ -70,6 +74,14 @@
                                 type="data"
                                 label="BAM File"
                         />
+                    </when>  
+                    <when value="bai">
+                        <param
+                                format="bai"
+                                name="BAI"
+                                type="data"
+                                label="BAI File"
+                        />
                     </when>     
                     <when value="bed">
                         <conditional name="bedChoice">