<tool id="pearStat" name="PEAR Statistics" version="1.0.0">
  <description>Generate paired-end reads overlap Statistic from PEAR log file</description>
    <version_command>
	    python ${__tool_directory__}/pear_stats.py --version
	</version_command>
  <command detect_errors="aggressive"><![CDATA[
      #set files=""
      #for $index,$file in enumerate($input):
        #set $files += str($file)+","
      #end for
      #set $files=$files[:-1]

      #set names=','.join( [ str( $name ) for $name in $input.keys() ])      

      python $__tool_directory__/pear_stats.py -i "$files" -s "$names" -o $output
   ]]> </command>
  <inputs>
    <param name="input" type="data_collection" format="txt" collection_type="list" label="PEAR LOG FILE"/>
  </inputs>
  <outputs>
    <!--<data format="tabular" name="output" label="${tool.name}.${input.display_name}"/>-->
    <data format="tabular" name="output" label="${tool.name}.log"/>
  </outputs>
  <tests>
    <test>
	  <param name="input">
	  	<collection type="list">
	  		   <element name="F3D0" value="F3D0.log" />
		   	   <element name="F3D1" value="F3D1.log" />
      	</collection>
	   </param>
      <output name="output" file="test_output.txt"/>
    </test>
  </tests>

  <help>
** what it does **

Creates summary log file by extracting "Assembled reads", "Discarded reads" and "Not assembled reads" from PEAR_ log.

.. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/doc.html

-----

=======
Example
=======

PEAR v0.9.6 [January 15, 2015]

Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593

==================================== =======================================
Field                                Parameter and output
------------------------------------ ---------------------------------------
Forward reads file.................: /mnt/galaxy/files/014/dataset_14938.dat
Reverse reads file.................: /mnt/galaxy/files/014/dataset_14939.dat
PHRED..............................: 33
Using empirical frequencies........: NO
Statistical method.................: OES
Maximum assembly length............: 999999
Minimum assembly length............: 50
p-value............................: 0.010000
Quality score threshold (trimming).: 0
Minimum read size after trimming...: 1
Maximal ratio of uncalled bases....: 1.000000
Minimum overlap....................: 10
Scoring method.....................: Scaled score
Threads............................: 2

Allocating memory..................: 200,000,000 bytes
Assemblying reads: 0%
Assemblying reads: 100%

Assembled reads ...................: 906 / 990 (91.515%)
Discarded reads ...................: 0 / 990 (0.000%)
Not assembled reads ...............: 84 / 990 (8.485%)
Assembled reads file...............: pear.assembled.fastq
Discarded reads file...............: pear.discarded.fastq
Unassembled forward reads file.....: pear.unassembled.forward.fastq
Unassembled reverse reads file.....: pear.unassembled.reverse.fastq
==================================== =======================================


-----

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

**Wrapper Authors**

QFAB Bioinformatics (support@qfab.org)

  </help>
  <citations>
       <citation type="doi">10.1093/bioinformatics/btt593</citation>
  </citations>
</tool>