<tool id="rename" name="reheader" version="1.0.0" force_history_refresh="True">
  <description>Rename sequence header in FASTQ file</description>
  <requirements>
    <requirement type="package" version="1.74">biopython</requirement>
  </requirements>
  <version_command>
	    python ${__tool_directory__}/reheader.py --version
  </version_command>
  <command detect_errors="aggressive">
        python  ${__tool_directory__}/reheader.py -n $inputfile.display_name -i $inputfile -o $output -d $log.files_path -l $log
  </command>

  <inputs>
    <param format="fastq,fastq.gz,fastq.bz2" name="inputfile" type="data" label="Short read data from your current history"/>
  </inputs>
  <outputs>
    <data name="output" format="fastq" label="${tool.name}.${inputfile.display_name}"/>
    <data name="log" format="txt" label="${tool.name}.${inputfile.display_name}.log"/>
  </outputs>
  <tests>
    <test>
      <param name="inputfile" value="F3D0_R1.fastq"/>
      <output name="outout" file="test_output.txt"/>
    </test>
  </tests>

  <help>
**what it does**

Renames sequence header in FASTQ file by appending SAMPLEFILENAME/1 to the end of the sequence header for the forward read or SAMPLEFILENAME_2 to the end of the sequence header for the reverse read using python_ and Biopython_

.. _python : https://www.python.org/downloads/release/python-370/
.. _Biopython : https://biopython.org/

-----

Forward Read
------------
**Input**

- **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042

**Output**

- **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/1

Reverse Read
------------

**Input**

- **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042

**Output**

- **sequence header** : @M03033:102:000000000-ATN0P:1:1101:9793:1042_Sample1/2

-----

=========
Resources
=========

**Wrapper Authors**

QFAB Bioinformatics (support@qfab.org)
  </help>

</tool>