<tool id="resync" name="resync: Paired-end resynchronization" version="1.0">
  <description>Resynchronize a pair of paired-end fastq files</description>
  <command interpreter="perl">
    resync.pl $input1 $input2 $output1 $output2
  </command>
  <inputs>
    <param name="input1" type="data" format="fastq" label="Input 1"/>
    <param name="input2" type="data" format="fastq" label="Input 2"/>
  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal"   description="Bad input dataset" />
  </stdio>
  <outputs>
    <data format_source="input1" name="output1" label="resync ${input1.name}"/>
    <data format_source="input2" name="output2" label="resync ${input2.name}"/>
  </outputs>
  <tests>
    <test>
      <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
      <param name="input2" ftype="fastq" value="reads2.fastqsanger" />
      <!-- synchronized files should remain unchanged -->
      <output name="output1" file="reads1.fastqsanger" />
      <output name="output2" file="reads2.fastqsanger" />
    </test>
    <test>
      <param name="input1" ftype="fastq" value="reads1.fastqsanger" />
      <param name="input2" ftype="fastq" value="reads_unsync_2.fastqsanger" />
      <output name="output1">
        <!-- unsynchronized files should remove unpaired read -->
        <assert_contents>
          <has_text text="@HWUSI-EAS1737:7:1:4411:1170#CAGATC/1" />
          <not_has_text text="@HWUSI-EAS1737:7:1:16187:1196#CAGATC/1" />
        </assert_contents>
      </output>
      <output name="output2">
        <!-- unsynchronized files should remove unpaired read -->
        <assert_contents>
          <has_text text="@HWUSI-EAS1737:7:1:4411:1170#CAGATC/2" />
          <not_has_text text="@HWUSI-EAS1737:7:1:16187:1196#CAGATC/2" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
Resynchronize a pair of paired-end fastq files. 

Reads in two potentially unsynchronized fastq files and writes out two synchronized fastq files. 

This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids.
Other types of read ID formats may cause a terminal error.

The synchronized files have properly paired reads, with singelton reads removed.

  </help>
</tool>