# HG changeset patch
# User dfornika
# Date 1580496201 0
# Node ID d2a5df8ada29c119adc449862b423158d3cb50d6
# Parent  627b2e75b1ad43975a957082ef79bf59aef68697
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/confindr/ commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"

diff -r 627b2e75b1ad -r d2a5df8ada29 confindr.xml
--- a/confindr.xml	Fri Jan 31 18:37:49 2020 +0000
+++ b/confindr.xml	Fri Jan 31 18:43:21 2020 +0000
@@ -9,6 +9,7 @@
     <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
+        mkdir input &&
         #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' &&
@@ -19,8 +20,8 @@
         #end if
         
         confindr.py 
-          --input_directory input \
-          --output_name output \
+          --input_directory input
+          --output_name output
 
     ]]></command>