/tools/emboss_5/emboss_primersearch.xml

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