Mercurial > repos > iuc > bedtools

diff getfastaBed.xml @ 58:ed6f66aed1f9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 29bd1be4655cd26052095a49a8e188d2572b703b"
author iuc
date Thu, 09 Sep 2021 13:02:16 +0000
parents 1d0a0d6a78b1
children 539958feb49c
line wrap: on
line diff
--- a/getfastaBed.xml	Wed Sep 01 11:02:26 2021 +0000
+++ b/getfastaBed.xml	Thu Sep 09 13:02:16 2021 +0000
@@ -11,13 +11,15 @@
     #set $fasta_file = $fasta_source.fasta
 #else
     #set $fasta_file = $fasta_source.fasta_id.fields.path
+    ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
 #end if
+ln -s '$fasta_file' 'input.fasta' &&
 bedtools getfasta
 $name
 $tab
 $strand
 $split
--fi '$fasta_file'
+-fi 'input.fasta'
 -bed '$input'
 -fo '$output'
     ]]></command>