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1 <?xml version="1.0"?>
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2 <tool id="p3_misa_1_parameter" name="Detect SSRs using MISA">
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3 <description>Detect simple sequence repeats using MISA</description>
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4 <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>
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5 <inputs>
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6 <param format="fasta" name="inputfastaFile" type="data" label="fasta Source file"/>
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7 <param name="definition_1" size="20" type="text" value="10" label="Min Repeats for Unit Size 1"> </param>
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8 <param name="definition_2" size="20" type="text" value="6" label="Min Repeats for Unit Size 2"> </param>
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9 <param name="definition_3" size="20" type="text" value="5" label="Min Repeats for Unit Size 3"> </param>
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10 <param name="definition_4" size="20" type="text" value="5" label="Min Repeats for Unit Size 4"> </param>
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11 <param name="definition_5" size="20" type="text" value="5" label="Min Repeats for Unit Size 5"> </param>
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12 <param name="definition_6" size="20" type="text" value="5" label="Min Repeats for Unit Size 6"> </param>
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13 <param name="interruptions" type="text" area="false" size="5" label="Interruptions:max_difference_between_2_SSRs" value="100" />
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14 </inputs>
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15 <outputs>
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16 <data format="tabular" name="misa_outputfile" />
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17 </outputs>
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18 <help>
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19
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20 .. class:: infomark
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21
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22 Detect simple sequence repeats using **MISA** - MIcroSAtellite identification tool
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23
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24 The MISA script was developed at IPK by Thomas Thiel
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25
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26 http://pgrc.ipk-gatersleben.de/misa/
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27
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28 CITATION
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29 ---------
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30
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31 Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
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32
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33 T. Thiel, W. Michalek, R. Varshney and A. Graner
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34
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35 THEORETICAL AND APPLIED GENETICS Volume 106, Number 3, 411-422
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36
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37 DOI: 10.1007/s00122-002-1031-0
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38
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39 **TIP**
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40 The primer design tool will work more predictably if fasta header lines are simplied to only include the sequence ID
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41
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42
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43
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44 </help>
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45
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46 </tool>
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