# HG changeset patch
# User p.lucas
# Date 1644848405 0
# Node ID cec55ef9cce59ec72ef8561fdc9b8290c0824b6a
# Parent  e93c20bad6b012135dbfd60c988126e6aa7d60a5
Use env clermont instead of requirements in the wrapper

diff -r e93c20bad6b0 -r cec55ef9cce5 ClermonTyping_wrapper.xml
--- a/ClermonTyping_wrapper.xml	Mon Feb 14 11:15:04 2022 +0000
+++ b/ClermonTyping_wrapper.xml	Mon Feb 14 14:20:05 2022 +0000
@@ -2,19 +2,10 @@
   <description>
     ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
   </description>
-  <requirements>
-    <requirement type="package" version="1.79">biopython</requirement>
-    <requirement type="package" version="2.12.0">blast</requirement>
-    <requirement type="package" version="2.17.1.1">pandoc</requirement>
-    <requirement type="package" version="2.1.2">r-readr</requirement>
-    <requirement type="package" version="1.0.7">r-dplyr</requirement>
-    <requirement type="package" version="1.2.0">r-tidyr</requirement>
-    <requirement type="package" version="1.37">r-knitr</requirement>
-    <requirement type="package" version="1.4.0">r-stringr</requirement>
-    <requirement type="package" version="2.11">r-markdown</requirement>
-  </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
+    source /home/galaxy/data/_conda/bin/activate Ab-HADDOCK;
+    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse;
+    source /home/galaxy/data/_conda/bin/deactivate;
   ]]></command>
   <inputs>
     <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>