# HG changeset patch
# User jpetteng
# Date 1515512296 18000
# Node ID 41301e1f075a84081d01dcdf97e100c312f3dee6
# Parent  c74c953c6b069550c54f84ac6653c7097dac8dce
Uploaded

diff -r c74c953c6b06 -r 41301e1f075a ecoli_serotyping/ectyper.xml
--- a/ecoli_serotyping/ectyper.xml	Sun Jan 07 15:20:17 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Tue Jan 09 10:38:16 2018 -0500
@@ -1,15 +1,7 @@
 <tool id="ectyper" name="ectyper" version="2.0">
     <requirements>
       <requirement type="package" version="3.6.3">python</requirement>
-      <requirement type="package">biopython</requirement>
-      <requirement type="package">blast</requirement>
-      <requirement type="package">samtools</requirement>
-      <requirement type="package">bcftools</requirement>
-      <requirement type="package">bowtie</requirement>
-      <requirement type="package">spades</requirement>
-      <requirement type="package">seqtk</requirement>
-      <requirement type="package">pandas</requirement>
-      <requirement type="package">mash</requirement>
+      <requirement type="package">ectyper</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if $jobtype.select == "asm"
@@ -21,7 +13,7 @@
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
 
-      python $__tool_directory__/ectyper/ectyper.py
+      python $__tool_directory__/bin/ectyper
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta