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<?xml version='1.0' encoding='utf-8'?>
<tool id="kat_@EXECUTABLE@" name="KAT @EXECUTABLE@" version="@VERSION@.2">
  <description>Filtering reads or k-mer from fasta file</description>
  <macros>
    <token name="@EXECUTABLE@">filter_seq</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" read.fastq && 

  kat filter seq

  --seq read.fastq
   
  #elif $single_or_paired.type == "paired"
  ln  "$single_or_paired.forward_pe" read_1.fastq && ln  "$single_or_paired.reverse_pe" read_2.fastq &&
  
  kat filter seq

  --seq read_1.fastq --seq2 read_2.fastq
  
  #else
  ln "$single_or_paired.fastq_collection.forward" read_1.fastq && ln  "$single_or_paired.fastq_collection.reverse" read_2.fastq &&
  
  kat filter seq

  --seq read_1.fastq --seq2 read_2.fastq
  
  #end if

  
  @THREADS@
  
  --mer_len $kmer
  
  $stats

  #if $invert_or_both.which == "invert":
     $invert_or_both.invert
  #elif $invert_or_both.which == "split":
     $invert_or_both.separate
  #end if
     
  -o reads
  'db.fasta'
  
  ]]></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="threshold" type="float" value='0.10000000000000001' label="Target Threshold" help="What percentage of the sequence needs to be covered with target k-mers to keep the sequence"/>

    <param name="stats" type="boolean" truevalue='--stats' falsevalue='' checked='False' label="Stats" help="Whether to emit statistics about quantity of found k-mers in each sequence."/>
    <conditional name="invert_or_both">
      <param name="which" type="select" label="Advance Options">
        <option value="none">No Advance</option>
        <option value="invert">Option 1</option>
        <option value="split">Option 2</option>
      </param>
      <when value="invert">
        <param name="invert" type="boolean" truevalue='--invert' falsevalue='' checked='True' label="Take k-mer not matching target" help="Whether to take k-mers outside region as selected content, rather than those inside."/>
      </when>
      <when value="split">
        <param name="separate" type="boolean" truevalue='--separate' falsevalue='' checked='True' label="Keep inside and outside of target(s) region" help="Whether to partition the k-mers into two sets, those inside region and those outside."/>
      </when>
      <when value="none">
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="fastqsanger" name="reads" label="Reads.fastq" from_work_dir="reads.in.fastq" >
      <filter> single_or_paired['type'] == "single" </filter>
    </data>
    <data format="fastqsanger" name="forward" label="forward_R1.fastq" from_work_dir="reads.in.R1.fastq" >
      <filter> single_or_paired['type'] == "paired"</filter>
    </data>
    <data format="fastqsanger" name="reverse" label="reverse_R2.fastq" from_work_dir="reads.in.R2.fastq" >
      <filter> single_or_paired['type'] == "paired"</filter>
    </data>


    <collection name="paired_reads" type="paired" label="Reads">
      <data name="forward" format="fastqsanger" from_work_dir="reads.in.R1.fastq" >
        <filter> single_or_paired['type'] == "collection"</filter>
      </data>
      <data name="reverse" format="fastqsanger" from_work_dir="reads.in.R2.fastq" >
        <filter> single_or_paired['type'] == "collection"</filter>
      </data>
    </collection>
    
    
    <data format="fastqsanger" name="outside_reads" label='Outside reads' from_work_dir="reads.out.fastq">
      <filter>invert_or_both['which'] == 'split' and invert_or_both['separate'] and single_or_paired['type'] == "single"</filter>
    </data>
    <data format="tabular" name="file_stats" label='Stats' from_work_dir="reads.stats">
      <filter>stats</filter>
    </data>

  </outputs>
  <tests>
    <test>
      <param name="input_se" 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>