<tool id="merged_paired_reads_wrapper" version="1.0" name="Merge paired reads">
  <requirements>
    <requirement type='package' version="1.7">sortmerna</requirement>
  </requirements>
  <description>Merges two fastq paired-reads files into one file.</description>
  <command>
merge-paired-reads.sh $input_reads1 $input_reads2 output_file.txt
  </command>
  <inputs>
    <param format="fastq" name="input_reads1" type="data"
	   label="First reads file (fastq)" help=""/>
    <param format="fastq" name="input_reads2" type="data"
	   label="Second reads file (fastq)" help=""/>
  </inputs>
  <outputs>
    <data format="fastq" name="output" from_work_dir="output_file.txt"
	  label="Merged reads from ${on_string} (fastq)">
    </data>
  </outputs>
  <stdio>
    <exit_code range="2" level="fatal"
	       description="Too few or two many arguments provided" />
  </stdio>
  <tests>
    <test>
      <param name="input_reads1" value="sortmerna_wrapper_accept1.fastq" />
      <param name="input_reads2" value="sortmerna_wrapper_other1.fastq" />
      <output name="output" file="merged-paired-reads_output.fastq" />
    </test>
  </tests>
  <help>
Merges two fastq paired-reads files into one file.

To run merge-paired-reads::

    bash merge-paired-reads.sh file1.fastq file2.fastq outputfile.fastq
  </help>
</tool>