<tool id="seqtk_nml_sample" name="seqTK Sample NML" version="1.0.0">
  <description>Runs seqTK sample if raw coverage is above user defined threshold </description>
  <requirements>
    <requirement type="package" version="1.2">seqtk</requirement>
    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" description="Unknown error has occured"/>
  </stdio>
  <command>
		perl  $__tool_directory__/seqtk_nml.pl --ref $fastar 

		#if $single_or_paired.type == "single"
			--type single
 			--forward $input_se
 			--cov $coverage 
			--out_forward $output
			--log $log
		#elif $single_or_paired.type == "paired"
	        --type paired
          	--forward $single_or_paired.forward_pe 
		--reverse $single_or_paired.reverse_pe
          	--cov $coverage 
		--out_forward $output 
		--out_reverse $output_rev
		--log $log
        #else
            collection
            $single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
            $coverage $output_collection.forward $output_collection.reverse
        #end if

  </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="txt" collection_type="paired" />
      </when>
    </conditional>
    <param name="fastar" type="data" label="Fasta Reference File" format="fasta" />
    <param name="coverage" type="integer" label="Desired Coverage" value="50" />
  </inputs>
  <outputs>
    <data format="fastqsanger" name="output" label="SubSampled Fastq" >
      <filter>single_or_paired['type']!="collection"</filter>
    </data>
    <data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
      <filter>single_or_paired['type']=="paired"</filter>
    </data>
    <collection name="output_collection" type="paired" label="SubSampled Fastqs">
      <data name="forward" format="fastqsanger"/>
      <data name="reverse" format="fastqsanger"/>
      <filter>single_or_paired['type']=="collection"</filter>
    </collection>
    <data format="txt" name="log" label="Log file"/>
  </outputs>
  
  <tests>
    <test>
      <param name="type" value="paired" />
      <param name="forward_pe" value="inputforward.fastq" />
      <param name="reverse_pe" value="inputreverse.fastq" />
      <param name="fastar" value="testref.fasta"/>
      <param name="coverage" value="50" />
      <output name="output" file="outputforward.fastq" />
      <output name="output_rev" file="outputreverse.fastq" />
      <output name="log" file="lognosample.log" />
    </test>
    <test>
      <param name="type" value="paired" />
      <param name="forward_pe" value="inputforward.fastq" />
      <param name="reverse_pe" value="inputreverse.fastq" />
      <param name="fastar" value="testref.fasta"/>
      <param name="coverage" value="25" />
      <output name="output" file="outputdownsamepleforward.fastq" />
      <output name="output_rev" file="outputdownsameplereverse.fastq" />
      <output name="log" file="logdownsample.log" />
    </test>
  </tests>
  <help>
What it does
============

Calculates raw coverage. If the raw coverage is greater than desired coverage, runs seqTK sample to generate downsampled reads. 


Usage
=====

**Parameters**
	- Fastq reads (single end, paired end, or paired end collection)
	- Fasta reference file

**Options**
	- Desired coverage (50)
  </help>
  <citations>
    <citation type="doi">doi.org/10.1371/journal.pone.0163962</citation>
  </citations>
</tool>