diff chira_extract.xml @ 18:e7ee3aadf1a5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 28963347255f1df6efaa8991ad9fc17f86b30a73"

--- a/chira_extract.xml	Wed Apr 07 12:43:02 2021 +0000
+++ b/chira_extract.xml	Fri Sep 24 06:49:19 2021 +0000
@@ -1,5 +1,6 @@
 <tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
     <description>extrat the chimeras</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -8,7 +9,9 @@
         #set $genomic_fasta = ''
         #if str($annotation.annot_choice) == "yes":
             #if str($annotation.fasta_source.fasta_source_selector) == 'history':
-                #set $genomic_fasta = $annotation.fasta_source.fasta
+                ## Avoid writing FASTA index to inputdir by symlinking 
+                ln -s '${$annotation.fasta_source.fasta}' genome.fa &&
+                #set $genomic_fasta = 'genome.fa'
             #else
                 #set $genomic_fasta = $annotation.fasta_source.fasta_id.fields.path
             #end if