comparison repex_tarean.xml @ 4:72c028e3e70e draft

Uploaded

3:d1f67a13b70f

<tool id="tarean_dev" name="Tandem Repeat Analyzer"  version="2.3.8" >
    <stdio>
      <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
      <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">repex_tarean_dev</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} &&

4:72c028e3e70e

<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.8" >
    <stdio>
      <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" />
      <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">shub://repeatexplorer/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 ${ReportFile.files_path} &&