<tool id="tophatstatsPE" name="Tophat Stats PE" version="1.0">
  <description>Calculate mapping statistics from Tophat BAM files.</description>
  <command interpreter="perl">tophatstatsPE.pl $hits $fastq > $output</command>
  <inputs>
    <param name="hits" type="data" format="bam" label="BAM file produced by Tophat"/>
    <param name="fastq" type="data" format="fastq" label="Fastq file used to produce the BAM file" />
  </inputs>
  <outputs>
    <data format="txt" name="output" />
  </outputs>
  <tests>
  </tests>
  <help>
**Tophat Stats PE**

This tool generates mapping statics from BAM files produced by
Tophat. For paired-end experiments only one of the read files (R1
or R2) needs to be provided.

**Example output:**

::

  Input files: /galaxy/database/files/001/dataset_1682.dat         /galaxy/database/files/001/dataset_1680.dat
  73538 total read pairs in fastq file
  14429 (19.62%) read pairs with only one read in the pair mapped (14262 with unique alignments)
  36461 (49.58%) read pairs mapped with correct orientation and insert size (36366 with unique alignments)
  12169 (16.55%) read pairs mapped with correct orientation but wrong insert size (12063 with unique alignments)
  0.458333333333333 (0.00%) read pairs mapped with wrong orientation but correct insert size (0 with unique alignments)
  10478.5416666667 (14.25%) read pairs with no mapping


**Credit**

John Garbe,  University of Minnesota

  </help>
</tool>