Mercurial > repos > jpetteng > ectyper

diff ecoli_serotyping/ectyper.xml @ 5:a202cc394af8 draft

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Hopefully fixed issue with finding ectyper.py
author jpetteng
date Fri, 05 Jan 2018 15:17:46 -0500
parents e07f3859a242
children 06e7c1355431
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--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 10:59:51 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Fri Jan 05 15:17:46 2018 -0500
@@ -1,7 +1,6 @@
 <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>
@@ -21,7 +20,7 @@
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
 
-      $__tool_directory__/ectyper.py
+      $__tool_directory__/ectyper/ectyper.py
       #if $jobtype.select == "asm"
         -m 4
         -i sample.fasta