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changeset 28:41301e1f075a draft

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Uploaded
author jpetteng
date Tue, 09 Jan 2018 10:38:16 -0500
parents c74c953c6b06
children 5442b9d2e5d1
files ecoli_serotyping/ectyper.xml
diffstat 1 files changed, 2 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- 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