--- a/ecoli_serotyping/ecoli_serotyping/ectyper.xml	Tue Jan 09 11:34:40 2018 -0500
+++ b/ecoli_serotyping/ecoli_serotyping/ectyper.xml	Tue Jan 09 11:34:51 2018 -0500
@@ -1,6 +1,7 @@
 <tool id="ectyper" name="ectyper" version="2.0">
     <requirements>
       <requirement type="package" version="3.6.3">python</requirement>
+      <requirement type="package">ectyper</requirement>
       <requirement type="package">biopython</requirement>
       <requirement type="package">blast</requirement>
       <requirement type="package">samtools</requirement>
@@ -8,7 +9,8 @@
       <requirement type="package">bowtie</requirement>
       <requirement type="package">spades</requirement>
       <requirement type="package">seqtk</requirement>
-#      <requirement type="package">mash</requirement>
+      <requirement type="package">pandas</requirement>
+      <requirement type="package">mash</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if $jobtype.select == "asm"
@@ -20,7 +22,7 @@
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
 
-      $__tool_directory__/bin/ectyper
+      python $__tool_directory__/bin/ectyper
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta