<?xml version='1.0' encoding='utf-8'?>
<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.1">
  <description> Estimates the coverage of each sequence in a file using K-mers from another sequence file(s).</description>
  <macros>
    <token name="@EXECUTABLE@">sect</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />
  <expand macro="version_command" />
  <command><![CDATA[

  cp "$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@
  
  $keep_counts
  
  -o results
  
  ]]></command>
  <inputs>
    <expand macro="macro_input" />

    <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
    <expand macro="macro_kmers" />
    <param name="keep_counts" type="boolean" falsevalue='--no_count_stats' truevalue='' checked='False' label="Fasta Count File" help="Produce a fasta style representation of the input sequence file containing K-mer coverage counts mapped across each sequence"/>
  </inputs>
  <outputs>
    <data format="tabular" name="stats" label='Stats' from_work_dir="results-stats.tsv" />
    <data format="txt" name="counts" label='Counts' from_work_dir="results-counts.cvg">
      <filter>keep_counts</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input_se" value="input.fastq" />
      <param name="db" value="db.fasta" />
      <param name="keep_counts" value="False" />
      <output file="kat-sect-stats.tsv" name="stats" />
    </test>
    <test>
      <param name="input_se" value="input.fastq" />
      <param name="db" value="db.fasta" />
      <param name="keep_counts" value="True" />
      <output file="kat-sect-stats.tsv" name="stats" />
      <output file="kat-sect-counts.cvg" name="counts" />
    </test>    
  </tests>
  <help><![CDATA[
  https://kat.readthedocs.io/en/latest/using.html#sect
]]>
  
  </help>
  <expand macro="citations" />
</tool>