Mercurial > repos > devteam > emboss_5
comparison emboss_primersearch.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
| author | devteam |
|---|---|
| date | Fri, 12 Aug 2016 19:17:10 -0400 |
| parents | |
| children | 0e2484b6829b |
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| 9:18a63c800a4d | 10:9b98d3d903c6 |
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| 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" 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 | |
| 37 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
| 38 | |
| 39 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>`_ | |
| 40 </help> | |
| 41 </tool> |