<tool id="fastq_subsampling_wrapper" name="Fastq subsampling" version="0.1">
  <description></description>
  <requirements>
	<requirement type="package" version="0.15">pysam</requirement>
  </requirements>
    <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <version_command>$__tool_directory__/fastq_subsampling.py -v</version_command>
  <command>
    $__tool_directory__/fastq_subsampling.py
	--galaxy
	#if $fastq.choice == "choice1"
	  -s '${fastq.single}'
	#end if
	#if $fastq.choice == "choice2"
	  -r '${fastq.forward}'
	  -l '${fastq.reverse}'
	#end if
	#if $fastq.choice == "choice3"
	  -r '${fastq.pairedfile.forward}'
	  -l '${fastq.pairedfile.reverse}'
	#end if
	#if str($coverage)
	  -c $coverage
	#end if
	$size
	&amp;> '$logfile'
  </command>
  <inputs>
	<conditional name="fastq" >
      <param name="choice" type="select" label="Type of reads to subsampling" help="" >
        <option value="choice1" selected="true">Single</option>
        <option value="choice2">Paired (separated)</option>
        <option value="choice3">Paired</option>
      </param>
      <when value="choice1">
		<param name="single" type="data" format="fastq,fastq.gz"
			   label="Single read file" help="Fastq(gz) format" />
      </when>
      <when value="choice2">
 		<param name="forward" type="data" format="fastq,fastq.gz"
			   label="Forward read file" help="Fastq(gz) format" />
		<param name="reverse" type="data" format="fastq,fastq.gz"
			   label="Reverse read file" help="Fastq(gz) format" />
      </when>
      <when value="choice3">
		<param name="pairedfile" type="data_collection" format="fastq,fastq.gz"
			   label="Paired of read files" help="Fastq(gz) format"
			   collection_type="paired" />
      </when>
    </conditional>
	<param name="size" type="integer" optional="false" value="6000000"
		   label="Size of the genome in bp" />
    <param name="coverage" type="integer" value="40" optional="true"
		   label="Mean coverage to sampling" />
  </inputs>

  <outputs>
    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
	<data name="singleout" format="fastqsanger.gz"
		  label="${tool.name} on ${fastq.single.name}"
		  from_work_dir="1.fastq.gz">
	  <filter>fastq['choice'] == "choice1"</filter>
	</data>
	<data name="forwardout" format="fastqsanger.gz"
		  label="${tool.name} on ${fastq.forward.name}"
		  from_work_dir="1.fastq.gz">
	  <filter>fastq['choice'] == "choice2"</filter>
	</data>
	<data name="reverseout" format="fastqsanger.gz"
		  label="${tool.name} on ${fastq.reverse.name}"
		  from_work_dir="2.fastq.gz">
	  <filter>fastq['choice'] == "choice2"</filter>
	</data>
	<collection name="paired_output" type="paired"
				label="${tool.name} on ${fastq.pairedfile.name}">
	  <data name="forward" format="fastqsanger.gz"
			from_work_dir="1.fastq.gz">
	  </data>
	  <data name="reverse" format="fastqsanger.gz"
			from_work_dir="2.fastq.gz">
	  </data>
	  <filter>fastq['choice'] == "choice3"</filter>
	</collection>
  </outputs>
  <tests>
	<test expect_num_outputs="3">
      <param name="choice" value="choice2" />
	  <param name="forward" value="input_R1.fastq.gz" />
	  <param name="reverse" value="input_R2.fastq.gz" />
	</test>
  </tests>
  <help>
**What it does**

Subsampling a single or a paired of fastq(.gz) file to a given coverage

**License and citation**

This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.

  </help>
  <citations>
  </citations>
</tool>