Mercurial > repos > john-mccallum > ssr_marker_design

<?xml version="1.0"?>
<tool id="p3_misa_1_parameter" name="Detect SSRs using MISA">
  <description>Detect simple sequence repeats using MISA</description>
  <command interpreter="perl">p3_misa_parameter.pl $inputfastaFile $misa_outputfile "1-$definition_1 2-$definition_2 3-$definition_3 4-$definition_4 5-$definition_5 6-$definition_6" "$interruptions" </command>
  <inputs>
    <param format="fasta" name="inputfastaFile" type="data" label="fasta Source file"/>
     <param name="definition_1" size="20" type="text" value="10" label="Min Repeats for Unit Size 1"> </param>
     <param name="definition_2" size="20" type="text" value="6" label="Min Repeats for Unit Size 2"> </param>
     <param name="definition_3" size="20" type="text" value="5" label="Min Repeats for Unit Size 3"> </param>
     <param name="definition_4" size="20" type="text" value="5" label="Min Repeats for Unit Size 4"> </param>
     <param name="definition_5" size="20" type="text" value="5" label="Min Repeats for Unit Size 5"> </param>
     <param name="definition_6" size="20" type="text" value="5" label="Min Repeats for Unit Size 6"> </param>
     <param name="interruptions" type="text" area="false" size="5" label="Interruptions:max_difference_between_2_SSRs" value="100" />
  </inputs>
  <outputs>
     <data format="tabular"  name="misa_outputfile" />
  </outputs>
<help>

.. class:: infomark

Detect simple sequence repeats using **MISA**  - MIcroSAtellite identification tool

The MISA  script was developed at IPK by Thomas Thiel

http://pgrc.ipk-gatersleben.de/misa/

CITATION
---------

Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)

T. Thiel, W. Michalek, R. Varshney and A. Graner

THEORETICAL AND APPLIED GENETICS Volume 106, Number 3, 411-422

DOI: 10.1007/s00122-002-1031-0

**TIP**
The primer design tool will work more predictably if fasta header lines are simplied to only include the sequence ID


</help>

</tool>
author	john-mccallum
date	Wed, 14 Sep 2011 23:57:57 -0400
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