# HG changeset patch
# User petr-novak
# Date 1697448132 0
# Node ID ba67036e6b3cbd6c54d9634cf867ac5707b806ef
# Parent  1eefa5b3e8b9591e543d85705f2a3cb175935741
Uploaded

diff -r 1eefa5b3e8b9 -r ba67036e6b3c repex_full_clustering.xml
--- a/repex_full_clustering.xml	Thu Jul 27 08:53:14 2023 +0000
+++ b/repex_full_clustering.xml	Mon Oct 16 09:22:12 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.1" >
+<tool id="repeatexplorer2" name="RepeatExplorer2 clustering: " version="2.3.8.2" >
     <stdio>
       <regex match="lastdb: can't open file: NEAR" source="stderr" level="fatal" description="Version of last is too old, use ver 956 or higher\n" />
       <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
@@ -12,6 +12,8 @@
    </requirements>
 <command>
       export PYTHONHASHSEED=0;
+      export TAREAN_CPU=\$GALAXY_SLOTS;
+      export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB;
       seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
 
       #if $advanced_options.advanced:
@@ -129,29 +131,11 @@
       <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
     </when>
   </conditional>
-
-       <conditional name="queue_definition">
-               <param name="queue_select" type="select" label="Select queue">
-                 <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
-                 <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
-                 <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
-               </param>
-               <when value="basic_fast_queue">
-                 <param name="queue_specification" type="text" label="Modify parameters (optional)"
-                        value="-l select=1:ncpus=10:mem=32gb:scratch_local=50gb -l walltime=48:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=4000000,TAREAN_CPU=4" />
-               </when>
-
-               <when value="long_slow_queue">
-                 <param name="queue_specification" type="text" label="Modify parameters (optional)"
-                        value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=336:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
-               </when>
-               <when value="extra_long_slow_queue">
-                 <param name="queue_specification" type="text" label="Modify parameters (optional)"
-                        value="-l select=1:ncpus=16:mem=112gb:scratch_local=50gb -l walltime=720:00:00 -q elixirre@pbs.elixir-czech.cz -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
-               </when>
-     </conditional>
- 
-
+  <param name="queue_select" type="select" label="Select queue">
+      <option value="basic_fast_queue">basic (max runtime 2 days, 4 GB RAM)</option>
+      <option value="long_slow_queue">long (max runtime 2 weeks, 64 GB RAM)</option>
+      <option value="extra_long_slow_queue">extra long (max runtime 4 weeks, 64 GB RAM)</option>
+  </param>
 
  </inputs>
     <outputs>