# HG changeset patch
# User petr-novak
# Date 1697447992 0
# Node ID 65d1a27e9339bcde4528ce673d1997d1f71a261b
# Parent  335d138b654b8b6c6f40016304d176c38761294d
planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty

diff -r 335d138b654b -r 65d1a27e9339 repex_full_clustering.xml
--- a/repex_full_clustering.xml	Fri May 27 12:00:40 2022 +0000
+++ b/repex_full_clustering.xml	Mon Oct 16 09:19:52 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" />
@@ -8,36 +8,13 @@
     </stdio>
     <description>Improved version or repeat discovery and characterization using graph-based sequence clustering</description>
    <requirements>
-     <requirement type="package">last</requirement>
-     <requirement type="package">imagemagick</requirement>
-     <requirement type="package">mafft</requirement>
-     <requirement type="package">blast</requirement>
-     <requirement type="package" version="0.9.29" >diamond</requirement>
-     <requirement type="package">blast-legacy</requirement>
-     <requirement type="package">r-igraph</requirement>
-     <requirement type="package">r-data.tree</requirement>
-     <requirement type="package">r-stringr</requirement>
-     <requirement type="package">r-r2html</requirement>
-     <requirement type="package">r-hwriter</requirement>
-     <requirement type="package">r-dt</requirement>
-     <requirement type="package">r-scales</requirement>
-     <requirement type="package">r-plotrix</requirement>
-     <requirement type="package">r-png</requirement>
-     <requirement type="package">r-plyr</requirement>
-     <requirement type="package">r-dplyr</requirement>
-     <requirement type="package">r-optparse</requirement>
-     <requirement type="package">r-dbi</requirement>
-     <requirement type="package">r-rsqlite</requirement>
-     <requirement type="package">r-rserve</requirement>
-     <requirement type="package">bioconductor-biostrings</requirement>
-     <requirement type="package" version="2.3.8.1">repex_tarean</requirement>
-     <requirement type="set_environment">REPEX</requirement>
-     <requirement type="set_environment">REPEX_VERSION</requirement>
-     <requirement type="package" version="0.9.1" >pyrserve</requirement>
+     <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
    </requirements>
-    <command >
+<command>
       export PYTHONHASHSEED=0;
-      \${REPEX}/seqclust --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup $paired --taxon $taxon
+      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:
       --mincl $advanced_options.size_threshold $advanced_options.keep_names $advanced_options.automatic_filtering  -D $advanced_options.blastx.options_blastx
@@ -60,21 +37,21 @@
       cat stdout.log >> ${log} ;
       echo "STDERR CONTENT:" >> ${log};
       cat stderr.log >> ${log} &amp;&amp;
-      \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
+      /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
       cd tarean_output &amp;&amp;
       zip -r  ${ReportArchive}.zip * &amp;&amp;
-      mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
+      mv  ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
       cp index.html ${ReportFile} &amp;&amp;
-      mkdir ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
-      cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
-      cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
-      cp *.png ${ReportFile.files_path}/ &amp;&amp;
-      cp *.csv ${ReportFile.files_path}/ &amp;&amp;
-      cp *.html ${ReportFile.files_path}/  &amp;&amp;
-      cp *.css ${ReportFile.files_path}/  &amp;&amp;
-      cp *.fasta ${ReportFile.files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
+      mkdir -p ${ReportFile.extra_files_path} &amp;&amp;
+      cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp;
+      cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp;
+      cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &amp;&amp;
+      cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
+      cp *.png ${ReportFile.extra_files_path}/ &amp;&amp;
+      cp *.csv ${ReportFile.extra_files_path}/ &amp;&amp;
+      cp *.html ${ReportFile.extra_files_path}/  &amp;&amp;
+      cp *.css ${ReportFile.extra_files_path}/  &amp;&amp;
+      cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
 
     </command>
  <inputs>
@@ -154,8 +131,11 @@
       <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
     </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>
diff -r 335d138b654b -r 65d1a27e9339 repex_tarean.xml
--- a/repex_tarean.xml	Fri May 27 12:00:40 2022 +0000
+++ b/repex_tarean.xml	Mon Oct 16 09:19:52 2023 +0000
@@ -6,36 +6,12 @@
       <exit_code range="1:" level="fatal" description="Error" />
     </stdio>
     <description>Identification of genomic tandem repeats from NGS data</description>
-    <requirements>
-      <requirement type="package">imagemagick</requirement>
-      <requirement type="package">mafft</requirement>
-      <requirement type="package">blast</requirement>
-      <requirement type="package" version="0.9.29">diamond</requirement>
-      <requirement type="package">blast-legacy</requirement>
-      <requirement type="package">r-igraph</requirement>
-      <requirement type="package">r-data.tree</requirement>
-      <requirement type="package">r-stringr</requirement>
-      <requirement type="package">r-r2html</requirement>
-      <requirement type="package">r-hwriter</requirement>
-      <requirement type="package">r-dt</requirement>
-      <requirement type="package">r-scales</requirement>
-      <requirement type="package">r-plotrix</requirement>
-      <requirement type="package">r-png</requirement>
-      <requirement type="package">r-plyr</requirement>
-      <requirement type="package">r-dplyr</requirement>
-      <requirement type="package">r-optparse</requirement>
-      <requirement type="package">r-dbi</requirement>
-      <requirement type="package">r-rsqlite</requirement>
-      <requirement type="package">r-rserve</requirement>
-      <requirement type="package">bioconductor-biostrings</requirement>
-      <requirement type="package" version="2.3.8.1">repex_tarean</requirement>
-      <requirement type="set_environment">REPEX</requirement>
-      <requirement type="set_environment">REPEX_VERSION</requirement>
-      <requirement type="package" version="0.9.1">pyrserve</requirement>
-    </requirements>
+   <requirements>
+     <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
+   </requirements>
   <command detect_errors="exit_code">
     export PYTHONHASHSEED=0;
-    \${REPEX}/seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${log} --cleanup --tarean_mode
+    seqclust --paired --sample ${read_sampling.sample} --output_dir=tarean_output --logfile=${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 :
@@ -53,21 +29,21 @@
     cat stdout.log >> ${log} ;
     echo "STDERR CONTENT:" >> ${log} ;
     cat stderr.log >> ${log} &amp;&amp;
-    \${REPEX}/stderr_filter.py stderr.log &amp;&amp;
+    /opt/repex_tarean/stderr_filter.py stderr.log &amp;&amp;
     cd tarean_output &amp;&amp;
     zip -r  ${ReportArchive}.zip * &amp;&amp;
     mv ${ReportArchive}.zip ${ReportArchive} &amp;&amp;
     cp index.html ${ReportFile} &amp;&amp;
-    mkdir ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents libdir ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &amp;&amp;
-    cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &amp;&amp;
-    cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
-    cp *.png ${ReportFile.files_path}/ &amp;&amp;
-    cp *.csv ${ReportFile.files_path}/ &amp;&amp;
-    cp *.html ${ReportFile.files_path}/  &amp;&amp;
-    cp *.css ${ReportFile.files_path}/  &amp;&amp;
-    cp *.fasta ${ReportFile.files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
+    mkdir -p ${ReportFile.extra_files_path} &amp;&amp;
+    cp -r --parents libdir ${ReportFile.extra_files_path} &amp;&amp;
+    cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &amp;&amp;
+    cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &amp;&amp;
+    cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &amp;&amp;
+    cp *.png ${ReportFile.extra_files_path}/ &amp;&amp;
+    cp *.csv ${ReportFile.extra_files_path}/ &amp;&amp;
+    cp *.html ${ReportFile.extra_files_path}/  &amp;&amp;
+    cp *.css ${ReportFile.extra_files_path}/  &amp;&amp;
+    cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log  &amp;&amp; rm -r ../tarean_output || :
 
     
   </command>
@@ -121,7 +97,28 @@
       </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>
+ 
+
 
   </inputs>
   <outputs>
diff -r 335d138b654b -r 65d1a27e9339 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 27 12:00:40 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0" ?>
-<tool_dependency>
-    <package name="repex_tarean" version="2.3.8.1">
-        <repository name="package_repex_tarean_2_3_8_1" owner="petr-novak" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="b876ecefd6d8"/>
-        <readme>
-      prepare repex database and scripts
-    </readme>
-    </package>
-</tool_dependency>
\ No newline at end of file