comparison repex_tarean.xml @ 7:65d1a27e9339 draft default tip

planemo upload commit ccbd120278facd9aa39c1c46665ee994ebd3cff2-dirty

6:335d138b654b

      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
      <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
      <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>
  <command detect_errors="exit_code">
    export PYTHONHASHSEED=0;
    \${REPEX}/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 :
     	  -d $advanced_options.custom_library.library extra_database
      #end if

    ${FastaFile} >stdout.log 2> stderr.log ;
    echo "STDOUT CONTENT:" >> ${log} ;
    cat stdout.log >> ${log} ;
    echo "STDERR CONTENT:" >> ${log} ;
    cat stderr.log >> ${log} &&
    \${REPEX}/stderr_filter.py stderr.log &&
    cd tarean_output &&
    zip -r  ${ReportArchive}.zip * &&
    mv ${ReportArchive}.zip ${ReportArchive} &&
    cp index.html ${ReportFile} &&
    mkdir ${ReportFile.files_path} &&
    cp -r --parents libdir ${ReportFile.files_path} &&
    cp -r --parents seqclust/clustering/superclusters ${ReportFile.files_path} &&
    cp -r --parents seqclust/clustering/clusters ${ReportFile.files_path} &&
    cp seqclust/clustering/hitsort.cls ${ReportFile.files_path}/seqclust/clustering/hitsort.cls &&
    cp *.png ${ReportFile.files_path}/ &&
    cp *.csv ${ReportFile.files_path}/ &&
    cp *.html ${ReportFile.files_path}/  &&
    cp *.css ${ReportFile.files_path}/  &&
    cp *.fasta ${ReportFile.files_path}/ 2>>$log  && rm -r ../tarean_output || :

    
  </command>

  <inputs>

          </param>
        </conditional>
      </when>
    </conditional>

    

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

7:65d1a27e9339

      <regex match="error" source="stderr" level="fatal" description="Unknown error" />
      <regex match="warning" source="stderr" level="warning" description="Unknown warning" />
      <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <description>Identification of genomic tandem repeats from NGS data</description>
   <requirements>
     <container type="singularity">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
   </requirements>
  <command detect_errors="exit_code">
    export PYTHONHASHSEED=0;
    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 :
     	  -d $advanced_options.custom_library.library extra_database
      #end if

    ${FastaFile} >stdout.log 2> stderr.log ;
    echo "STDOUT CONTENT:" >> ${log} ;
    cat stdout.log >> ${log} ;
    echo "STDERR CONTENT:" >> ${log} ;
    cat stderr.log >> ${log} &&
    /opt/repex_tarean/stderr_filter.py stderr.log &&
    cd tarean_output &&
    zip -r  ${ReportArchive}.zip * &&
    mv ${ReportArchive}.zip ${ReportArchive} &&
    cp index.html ${ReportFile} &&
    mkdir -p ${ReportFile.extra_files_path} &&
    cp -r --parents libdir ${ReportFile.extra_files_path} &&
    cp -r --parents seqclust/clustering/superclusters ${ReportFile.extra_files_path} &&
    cp -r --parents seqclust/clustering/clusters ${ReportFile.extra_files_path} &&
    cp seqclust/clustering/hitsort.cls ${ReportFile.extra_files_path}/seqclust/clustering/hitsort.cls &&
    cp *.png ${ReportFile.extra_files_path}/ &&
    cp *.csv ${ReportFile.extra_files_path}/ &&
    cp *.html ${ReportFile.extra_files_path}/  &&
    cp *.css ${ReportFile.extra_files_path}/  &&
    cp *.fasta ${ReportFile.extra_files_path}/ 2>>$log  && rm -r ../tarean_output || :

    
  </command>

  <inputs>

          </param>
        </conditional>
      </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="TAREAN log file"/> 
	  <data name="ReportArchive" format="zip" label="TAREAN Archive with HTML report from data ${FastaFile.hid}"/>