comparison repex_full_clustering.xml @ 5:397394c00bf7 draft

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4:72c028e3e70e

      <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
      <param name="assembly_min_cluster_size" type="integer" label="Minimal cluster size for assembly" value="5" min="2" max="100"/>
    </when>
  </conditional>

  

 </inputs>
    <outputs>
	<data name="log" format="txt" label="RepeatExplorer2 - log file"/> 
	<data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/> 

5:397394c00bf7

      <param name="keep_names" label="Keep original read names" type="boolean" truevalue="--keep_names" falsevalue="" checked="false" help="By default, reads are renamed using integers. Use this option to keep original names."/>
      <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 [e-mail] -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 [e-mail] -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 [e-mail] -v TAREAN_MAX_MEM=64000000,TAREAN_CPU=15" />
               </when>
     </conditional>
 


 </inputs>
    <outputs>
	<data name="log" format="txt" label="RepeatExplorer2 - log file"/> 
	<data name="ReportArchive" format="zip" label="RepeatExplorer2 - Archive with HTML report from data ${FastaFile.hid}"/>