<tool id="kat_sect" name="KAT Sect" version="1.3.0">
  <description> SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</description>
  <requirements>
    <requirement type="package" version="2.3.1">kat</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[

  ln "$db" db.fasta &&
  #if $single_or_paired.type == "single"
    ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 
    kat sect 'db.fasta'
    "$single_or_paired.input_se.element_identifier".fastq
  #elif $single_or_paired.type == "paired"
    ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
    kat sect 'db.fasta'
    "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq
  #else
    ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
    kat sect 'db.fasta'
    "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
  #end if  
  --threads \${GALAXY_SLOTS:-4}
  -o reads
  
  ]]></command>
  <inputs>
    <conditional name="single_or_paired">
      <param name="type" type="select" label="Read type">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
        <option value="collection">Collection Paired-end</option>
      </param>
      <when value="single">
        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
      </when>
      <when value="paired">
        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
      </when>
      <when value="collection">
        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
      </when>
    </conditional>
    <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
  </inputs>
  <outputs>
    <data format="tabular" name="reads" label='Reads' from_work_dir="reads-stats.tsv" />
  </outputs>
  <tests>
    <test>
      <param name="input" value="input.fastq" />
      <param name="db" value="db.fasta" />
      <output file="matched.fastq" ftype="fastqsanger" name="reads" />
    </test>
  </tests>
  <help><![CDATA[
http://kat.readthedocs.io/en/latest/using.html#filtering-tools
]]>
  
  </help>
  <citations>
  </citations>
</tool>