comparison repex_tarean.xml @ 19:3d0ba5734776 draft

Uploaded

18:4308d3e572ee

<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.8.3" >
    <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">library://repeatexplorer/default/repex_tarean:0.3.8-dbaa07f</container>
   </requirements>
  <command detect_errors="exit_code">
    export PYTHONHASHSEED=0;
    export TAREAN_CPU=\$GALAXY_SLOTS;
    export TAREAN_MAX_MEM=\$GALAXY_MEMORY_MB;
    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

19:3d0ba5734776

<tool id="tarean" name="Tandem Repeat Analyzer"  version="2.3.9.1" >
    <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">library://repeatexplorer/default/repex_tarean:0.3.9-579a65d</container>
   </requirements>
  <command detect_errors="exit_code">
    export PYTHONHASHSEED=0;
    export TAREAN_CPU=\$GALAXY_SLOTS;
    export TAREAN_MAX_MEM=\$((GALAXY_MEMORY_MB*1024));
    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