Mercurial > repos > iuc > bioext_bam2msa

diff bam2msa.xml @ 8:27673f5b5343 draft

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planemo upload for repository https://github.com/davebx/bioext-gx/ commit 473fd4bfc9bc6dc149978013545525529978b988
author iuc
date Sun, 25 Feb 2024 19:30:19 +0000
parents a68cb16fa1a0
children
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--- a/bam2msa.xml	Mon Nov 08 11:40:50 2021 +0000
+++ b/bam2msa.xml	Sun Feb 25 19:30:19 2024 +0000
@@ -3,18 +3,18 @@
     <description>to FASTA multiple sequence alignment</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
     </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 &&
+        ln -sf '$input' input_bam &&
+        ln -sf '$input.metadata.bam_index' input_bam.bai &&
         bam2msa
             #if $region_start and $region_end:
                 -r $region_start:$region_end
             #end if
-            'input_bam' '$output'
+            'input_bam'
+            '$output'
         ]]></command>
     <inputs>
         <param name="input" type="data" format="bam,sam" label="Input BAM file"/>