--- a/seqsero2.xml	Sat Sep 07 14:13:54 2019 -0400
+++ b/seqsero2.xml	Sat Sep 07 14:20:44 2019 -0400
@@ -12,32 +12,34 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       echo "SeqSero 2 v. 1.0.1" ;
+      mkdir ./output;
+      cp $__tool_directory__/SalmID.py output/;      
+      cp $__tool_directory__/invA_mers_dict output/;      
+      cp $__tool_directory__/rpoB_mers.dict output/;      
 
       #if $reads.reads_select == 'history'
-      #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
-      #set $forward = $reads.forward
-      #set $reverse = $reads.reverse
+        #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
+        #set $forward = $reads.forward
+        #set $reverse = $reads.reverse
       #else
-      #set $name = $reads.coll.name.replace(' ', '_')
-      #set $forward = $reads.coll.forward
-      #set $reverse = $reads.coll.reverse
+        #set $name = $reads.coll.name.replace(' ', '_')
+        #set $forward = $reads.coll.forward
+        #set $reverse = $reads.coll.reverse
       #end if
-        echo $name ;
-        echo "-=-=-=-=-" ;
+      echo $name ;
+      echo "-=-=-=-=-" ;
       #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
         gunzip -c $forward > forward.fastq;
-      #set $forward = './forward.fastq'
+        #set $forward = './forward.fastq'
       #end if
       #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
         gunzip -c $reverse > reverse.fastq;
-      #set $reverse = './reverse.fastq'
+        #set $reverse = './reverse.fastq'
       #end if
-        ln -s $forward ${name}_1.fastq;
-        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
+      ln -s $forward ${name}_1.fastq;
+      ln -s $reverse ${name}_2.fastq;
+      touch output/SeqSero_log.txt ;
+      python $__tool_directory__/SeqSero2_package.py
         -p \${GALAXY_SLOTS:-4}
         -t 2
         -m $mode