Mercurial > repos > iuc > bedtools

changeset 40:a68aa6c1204a 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 13:04:07 +0000
parents 3e38c9b3214f
children 7ab85ac5f64b
files getfastaBed.xml nucBed.xml
diffstat 2 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/getfastaBed.xml	Wed Sep 01 11:04:15 2021 +0000
+++ b/getfastaBed.xml	Thu Sep 09 13:04:07 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>
--- a/nucBed.xml	Wed Sep 01 11:04:15 2021 +0000
+++ b/nucBed.xml	Thu Sep 09 13:04:07 2021 +0000
@@ -7,6 +7,7 @@
     <expand macro="requirements" />
     <expand macro="stdio" />
     <command><![CDATA[
+ln -s '$fasta' 'input.fasta' &&
 bedtools nuc
 $s
 $seq
@@ -14,7 +15,7 @@
     -pattern '$pattern'
     $C
 #end if
--fi '$fasta'
+-fi 'input.fasta'
 -bed '$input'
 > '$output'
     ]]></command>