<tool id="RMsearch2" name="RepeatMasker custom search2" version="1.0.3">

  <description>Scan clustering results using RepeatMasker against custom database of repeats</description>
  <requirements>
    <requirement type="package" version="4.0.7">repeatmasker</requirement> 
    <requirement type="package" version="3.6">python</requirement> 
    <requirement type="package" version="2.3.2">r-r2html</requirement>
    <requirement type="package" version="2.54.0">bioconductor-biostrings</requirement>
  </requirements>

  <command>

    python3 ${__tool_directory__}/RM_custom_search.py -i $input_zip -d $RMdatabase -g $__root_dir__ -r $output_html;

  </command>

  <inputs>
    <param format="zip" type="data" name="input_zip" label="RepeatExplorer output data archive" help="Zip archive obtained from previouse Graph-based sequence clustering"/>
    <param name="RMdatabase" format="fasta" type="data" label="Library of repeats" help="Library of repeats as DNA sequences in fasta format. The recommended format for IDs in a custom library is : '>reapeatname#class/subclass'"/>
  </inputs>
  
  <outputs>
    <data format="html" name="output_html" label="HTML summary of custom database ${RMdatabase.hid} search on dataset ${input_zip.hid} " />
  </outputs>

  <help>
    **What it does**

    Use this tool if you want to scan previous clustering result with custom database of repeats using repeatmasker. 
    
  </help>
</tool>