# HG changeset patch
# User iuc
# Date 1632466159 0
# Node ID e7ee3aadf1a5fa58d6e2b7fe6eccd2cba4672f5f
# Parent  8b2c1d1556ac4f994615293a3b343b5e6946f23d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 28963347255f1df6efaa8991ad9fc17f86b30a73"

diff -r 8b2c1d1556ac -r e7ee3aadf1a5 chira_extract.xml
--- 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
diff -r 8b2c1d1556ac -r e7ee3aadf1a5 macros.xml
--- a/macros.xml	Wed Apr 07 12:43:02 2021 +0000
+++ b/macros.xml	Fri Sep 24 06:49:19 2021 +0000
@@ -1,6 +1,11 @@
 <macros>
     <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
     <token name="@TOOL_VERSION@">1.4.3</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">chira</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">chira</requirement>