# HG changeset patch
# User jpetteng
# Date 1515263543 18000
# Node ID 5b52b3842765960174020983abb69b301242e165
# Parent  148199949636176f3ebf26e2c2052f047cfc922f
Uploaded

diff -r 148199949636 -r 5b52b3842765 ecoli_serotyping/ectyper.xml
--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 16:25:18 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Sat Jan 06 13:32:23 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>
@@ -19,9 +20,7 @@
         ln -s $jobtype.fastq1 sample_1.fastq;  
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
-	PYTHONPATH=\$PATHONPATH:$__tool_directory__/ecytper/
-
-      $__tool_directory__/ectyper/ectyper.py
+		ectyper.py
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta