<tool id="ClermonTyping" name="ClermonTyping" version="1">
  <description>
    ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
  </description>
  <requirements>
    <requirement type="package" version="1.79">biopython</requirement>
    <requirement type="package" version="2.12.0">blast</requirement>
    <requirement type="package" version="2.17.1.1">pandoc</requirement>
    <requirement type="package" version="2.1.2">r-readr</requirement>
    <requirement type="package" version="1.0.7">r-dplyr</requirement>
    <requirement type="package" version="1.2.0">r-tidyr</requirement>
    <requirement type="package" version="1.37">r-knitr</requirement>
    <requirement type="package" version="1.4.0">r-stringr</requirement>
    <requirement type="package" version="2.11">r-markdown</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    /home/galaxy/ClermonTyping/clermonTyping.sh --fasta ${input} --name Analyse
  ]]></command>
  <inputs>
    <param name="input" format="fasta" type="data" label="Select contigs file in fasta format." help="Fasta format containing contigs."/>
  </inputs> 
  <outputs>
    <data name="html" format="html" label="html output file" from_work_dir="Analyse/Analyse.html"/>
    <data name="phylogroup" format="tsv" label="Phylogroup found" from_work_dir="Analyse/Analyse_phylogroups.txt"/>
  </outputs>
  <help>
    Script usage :
      -h		: print this message and exit
      -v		: print the version and exit
      --fasta		: fasta contigs file(s). If multiple files, they must be separated by an arobase (@) value
      --name		: name for this analysis (optional)
      --threshold	: option for ClermontTyping, do not use contigs under this size (optional)
      --minimal		: output a minimal set of files (optional)
      --fastafile	: file with path of fasta contig file.  One file by line (optional)
      --summary		: file with path of *_phylogroups.txt. One file by line (optional)
  </help>
</tool>