# HG changeset patch
# User petr-novak
# Date 1578301231 18000
# Node ID c0ae68651c11b7b82db6fe2a8da7ff7708a9aa72
# Parent  394a697ffa4930ebf3a3b2c6f20512d984632213
Uploaded

diff -r 394a697ffa49 -r c0ae68651c11 repex_tarean.xml
--- a/repex_tarean.xml	Mon Jan 06 03:59:39 2020 -0500
+++ b/repex_tarean.xml	Mon Jan 06 04:00:31 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="tarean" name="Tandem Repeat Analyzer" >
+<tool id="tareanx" name="Tandem Repeat Analyzer"  version="2.3.6" >
     <stdio>
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
       <regex match="error" source="stderr" level="fatal" description="Unknown error" />
@@ -9,6 +9,7 @@
     <requirements>
       <requirement type="package" version="3.7">python</requirement>
       <requirement type="package" version="0.9.1" >pyrserve</requirement>
+      <requirement type="package">last</requirement>
       <requirement type="package">mafft</requirement>
       <requirement type="package">imagemagick</requirement>
       <requirement type="package">blast</requirement>
@@ -30,11 +31,12 @@
       <requirement type="package">r-rsqlite</requirement>
       <requirement type="package">r-rserve</requirement>
       <requirement type="package">bioconductor-biostrings</requirement>
+      <requirement type="package" version="1.0">repex_tarean</requirement>
+      <requirement type="set_environment">REPEX</requirement>
     </requirements>
-
   <command detect_errors="exit_code">
     export PYTHONHASHSEED=0;
-    ${__tool_directory__}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
+    \${REPEX}/seqclust --paired --sample ${sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
     #if $advanced_options.advanced:
       --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering -M $advanced_options.merging
       #if $advanced_options.custom_library.options_custom_library :