# HG changeset patch
# User iuc
# Date 1632595973 0
# Node ID a68cb16fa1a0ae2110fd32bcbc8973fee4892701
# Parent  b226e0c805a584a50a3c979630a893c97e8d41b5
"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"

diff -r b226e0c805a5 -r a68cb16fa1a0 bam2msa.xml
--- a/bam2msa.xml	Fri Aug 20 21:03:56 2021 +0000
+++ b/bam2msa.xml	Sat Sep 25 18:52:53 2021 +0000
@@ -7,11 +7,14 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
+        ## avoid bam2msa to create .bai in inputdir
+        ln -s '$input' input_bam &&
+        ln -s '$input.metadata.bam_index' input_bam.bai &&
         bam2msa
             #if $region_start and $region_end:
                 -r $region_start:$region_end
             #end if
-            '$input' '$output'
+            'input_bam' '$output'
         ]]></command>
     <inputs>
         <param name="input" type="data" format="bam,sam" label="Input BAM file"/>