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changeset 1:1ba09e41181d draft

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MAJ way to access to resfinder
author p.lucas
date Thu, 07 Apr 2022 07:01:07 +0000
parents e94c6265e7e1
children 05f2df368f39
files Resfinder_wrapper.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/Resfinder_wrapper.xml	Wed Apr 06 16:11:02 2022 +0000
+++ b/Resfinder_wrapper.xml	Thu Apr 07 07:01:07 2022 +0000
@@ -120,7 +120,7 @@
     <requirement type="package" version="1.2.11">zlib</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
-    ln -s '${input}' ${_input_file} && python3 $__tool_directory__/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$y" --acquired --point -ifa $_input_file -db_res $__tool_directory__/resfinder/db_resfinder/ -db_point $__tool_directory__/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
+    ln -s '${input}' ${_input_file} && python3 /home/galaxy/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$y" --acquired --point -ifa $_input_file -db_res /home/galaxy/resfinder/db_resfinder/ -db_point /home/galaxy/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
   ]]></command>
   <inputs>
     <param format="fasta" name="input" type="data" label="FASTA file : "/>