# HG changeset patch
# User yating-l
# Date 1489592430 14400
# Node ID d917e081decd2082bda9d3d3504c5cd8db979195
# Parent  5580dbf2a31c5653362de92391fe28ac7449148a
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

diff -r 5580dbf2a31c -r d917e081decd jbrowse_hub.xml
--- a/jbrowse_hub.xml	Wed Mar 15 11:36:09 2017 -0400
+++ b/jbrowse_hub.xml	Wed Mar 15 11:40:30 2017 -0400
@@ -26,7 +26,6 @@
             #end if
             #if $f.formatChoice.format_select == 'bam'
                 --bam $f.formatChoice.BAM
-                --bai $f.formatChoice.BAM.metadata.bam_index
             #end if
             #if $f.formatChoice.format_select == 'gff3_transcript'
                 --gff3_transcript $f.formatChoice.GFF3_transcript
@@ -56,7 +55,6 @@
                 <conditional name="formatChoice">
                     <param name="format_select" type="select" label="Format">
                         <option value="bam" selected="true">BAM</option>
-                        <option value="bai">BAI (BAM index)</option>
                         <option value="bed">BED</option>
                         <option value="blastxml">BLASTXML</option>
                         <option value="bigwig">BIGWIG</option>
@@ -72,14 +70,6 @@
                                 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">