Mercurial > repos > iuc > bioext_bam2msa

changeset 4:a68cb16fa1a0 draft

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"planemo upload for repository https://github.com/davebx/bioext-gx/ commit 0c2133318563cdb508cb5561e95c9066bc17345f"
author iuc
date Sat, 25 Sep 2021 18:52:53 +0000
parents b226e0c805a5
children 405ed9ad53ab
files bam2msa.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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"/>