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1 <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
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2 <description>Searches DNA sequences for matches with primer pairs</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>Main sequences</label>
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8 </param>
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9 <param format="data" name="input2" type="data">
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10 <label>Primer file</label>
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11 </param>
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12 <param name="mismatchpercent" size="4" type="text" value="0">
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13 <label>Allowed percent mismatch</label>
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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data format="primersearch" name="out_file1" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input1" value="2.fasta"/>
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22 <param name="input2" value="emboss_primersearch.fasta"/>
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23 <param name="mismatchpercent" value="0"/>
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24 <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
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25 </test>
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26 </tests>
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27 <help>
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28
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29 You can view the original documentation here_.
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30
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31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
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32 </help>
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33 </tool>
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