/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  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Main sequences</label>
 8    </param>
 9    <param format="data" name="input2" type="data">
10      <label>Primer file</label>
11    </param>
12    <param name="mismatchpercent" size="4" type="text" value="0">
13      <label>Allowed percent mismatch</label>
14    </param>
15  </inputs>
16  <outputs>
17    <data format="primersearch" name="out_file1" />
18  </outputs>
19  <tests>
20    <test>
21      <param name="input1" value="2.fasta"/>
22      <param name="input2" value="emboss_primersearch.fasta"/>
23      <param name="mismatchpercent" value="0"/>
24      <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
25    </test>
26  </tests>
27  <help>
28
29    You can view the original documentation here_.
30    
31    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
32
33------
34
35**Citation**
36
37If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
38  </help>
39</tool>