<tool id="extract_archive_merge" name="Decompress an archive" version="1.0.0" force_history_refresh="True" >
  <description>in zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2 format</description>
  <command interpreter="python">
	
extract_archive_and_merge.py $input_archive "$input_archive.display_name" $log $log.id $__new_file_path__ $options_merge.merge
#if str( $options_merge.merge ) == 'true'
${options_merge.rm_header}
$concat
#end if

  </command>
 <inputs>
    <param name="input_archive" type="data" format="zip,tar.gz,tar.bz2,fastq.gz,fastq.bz2" label="Archive name" help="Accepts zip, tar.gz and tar.bz2" />
    <conditional name="options_merge">
    <param name="merge" type="select" format="text" label="Merges all files into one">
	<option value="false">No</option>
	<option value="true">Yes</option>
    </param>
    <when value="false">
    </when>
    <when value="true">
	<param name="rm_header" type="integer" value="0" label="Header lines to delete" help="number of lines to delete at the beginning of each file"/>
    </when>
    </conditional>
 </inputs>
 <outputs>
    <data format="txt" name="log" label="decompress_an_archive.log" />
    <data format="txt" name="additional" label="additional file with ${tool.name}" hidden="true">
          <discover_datasets pattern="__designation_and_ext__" directory="decompress_files" visible="true" />
    </data>  

    <data format="txt" name="concat" label="merge_file">
       <filter>(options_merge['merge'] == 'true')</filter>
    </data>
 </outputs>
 <help>
**Tool documentation**

This tool simply decompresses an archive file (zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2) and merges all files into only one. 
If the merge option is enabled, you can delete as many header lines as you need.

WARNING : the filename should not have special characters (space, brackets, ...), please rename it!!!

--------

**Created and integrated by:**

Cyril Monjeaud 

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)

support@genouest.org

If you use this tool in Galaxy, please cite :

`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
 </help>
</tool>