parse_primersearch.xml

<?xml version="1.0"?>
<tool id="parse_primersearch_1" name="Parse Primer search">
  <description>Parse EMBOSS primer search output to tabular </description>
  <command interpreter="perl">parse_primersearch.pl $inputPrimersearchFile $outputfile </command>
  <inputs>
    <param format="primersearch" name="inputPrimersearchFile" type="data" label="Primersearch  output file"/>
  </inputs>
  <outputs>

     <data format="tabular" name="outputfile" />
  </outputs>
<help>

.. class:: infomark

**TIP**

This tool parses EMBOSS primersearch_ output into columnar format suitable for use as interval 



Columns are:

1. Primer set ID
2. Hit ID
3. Number of mismatches
4. Amplimer start
5. Amplimer end
6. Amplicon length


----

**Example**

*output*

::

 ACP032  isotig07062     0       214     363     149
 ACP223  isotig04647     0       362     574     212
 ACP224  isotig04647     0       303     519     216
 ACP225  isotig04647     0       153     355     202
 ACP363  isotig10393     0       93      193     100
 ACP394  isotig00271     0       894     986     92
 ACP394  isotig00273     0       805     897     92
 ACP440  isotig05277     0       506     601     95
 ACP615  isotig00271     0       894     978     84
 ACP615  isotig00273     0       805     889     84
 AJK295  isotig06005     0       182     651     469


.. _primersearch: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html

-----------------------

*If you use this tool please cite:*

A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: 
Application For  Development Of A Framework Linkage Map In Bulb Onion (*Allium cepa* L.)
(2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, 
Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum


</help>
</tool>