/tools/emboss_5/emboss_primersearch.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 39 lines · 34 code · 5 blank · 0 comment · 0 complexity · 22aeb319314bc07d8e0beed235a8e7b1 MD5 · raw file
- <tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
- <description>Searches DNA sequences for matches with primer pairs</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>Main sequences</label>
- </param>
- <param format="data" name="input2" type="data">
- <label>Primer file</label>
- </param>
- <param name="mismatchpercent" size="4" type="text" value="0">
- <label>Allowed percent mismatch</label>
- </param>
- </inputs>
- <outputs>
- <data format="primersearch" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="2.fasta"/>
- <param name="input2" value="emboss_primersearch.fasta"/>
- <param name="mismatchpercent" value="0"/>
- <output name="out_file1" file="emboss_primersearch_out.primersearch"/>
- </test>
- </tests>
- <help>
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html
-
- ------
-
- **Citation**
-
- If 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>