# HG changeset patch
# User dfornika
# Date 1580497754 0
# Node ID 202247a3c969b5c7c53d98d407f5e3610b9cb6b7
# Parent  2ab80b982480c86bb6d7ca3004e97f8fefb38f47
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"

diff -r 2ab80b982480 -r 202247a3c969 confindr.xml
--- a/confindr.xml	Fri Jan 31 18:53:30 2020 +0000
+++ b/confindr.xml	Fri Jan 31 19:09:14 2020 +0000
@@ -10,6 +10,7 @@
 
     <command detect_errors="exit_code"><![CDATA[
         mkdir input &&
+        mkdir databases &&
         #if str( $reads_input.reads_input_selector ) == "paired"
           ln -s '$reads_input.reads_1' 'input/reads_R1.fastq' &&
           ln -s '$reads_input.reads_2' 'input/reads_R2.fastq' &&
@@ -20,8 +21,10 @@
         #end if
         
         confindr.py 
-          --input_directory input
-          --output_name output
+          --threads \${GALAXY_SLOTS:-1}
+          --databases 'databases'
+          --input_directory 'input'
+          --output_name 'output'
 
     ]]></command>