# HG changeset patch
# User estrain
# Date 1567879735 14400
# Node ID 55d2ec45737f14e39533648e4b955f0d47de6da0
# Parent  4e1596ee5c94a5e05a376d89c047e06feddcf22c
Uploaded

diff -r 4e1596ee5c94 -r 55d2ec45737f seqsero2.xml
--- a/seqsero2.xml	Sat Sep 07 13:56:48 2019 -0400
+++ b/seqsero2.xml	Sat Sep 07 14:08:55 2019 -0400
@@ -12,9 +12,6 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       echo "SeqSero 2 v. 1.0.1" ;
-      cp $__tool_directory__/SalmID.py .;
-      cp $__tool_directory__/invA_mers_dict .;
-      cp $__tool_directory__/rpoB_mers_dict .;
 
       #if $reads.reads_select == 'history'
       #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
@@ -39,6 +36,7 @@
         ln -s $reverse ${name}_2.fastq;
         mkdir ./output;
         touch output/SeqSero_log.txt ;
+        python $__tool_directory__/SalmID.py -i ${name}_1.fastq > salmid_output.txt;
         python $__tool_directory__/SeqSero2_package.py
         -p \${GALAXY_SLOTS:-4}
         -t 2