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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author | devteam |
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date | Fri, 12 Aug 2016 19:17:10 -0400 |
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children | 0e2484b6829b |
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<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0"> <description>Looks for inverted repeats in a nucleotide sequence</description> <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> <inputs> <param format="fasta" name="input1" type="data"> <label>Sequences</label> </param> <param name="minpallen" type="text" value="10"> <label>Minimum length of palindrome</label> </param> <param name="maxpallen" type="text" value="100"> <label>Maximum length of palindrome</label> </param> <param name="gaplimit" type="text" value="100"> <label>Maximum gap between repeated regions</label> </param> <param name="nummismatches" type="text" value="0"> <label>Number of mismatches allowed</label> </param> <param name="overlap" type="select"> <label>Report overlapping matches</label> <option value="yes">Yes</option> <option value="no">No</option> </param> </inputs> <outputs> <data format="palindrome" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="2.fasta"/> <param name="minpallen" value="10"/> <param name="maxpallen" value="100"/> <param name="gaplimit" value="100"/> <param name="nummismatches" value="0"/> <param name="overlap" value="yes"/> <output name="out_file1" file="emboss_palindrome_out.palindrome"/> </test> </tests> <help> .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html ------ **Citation** 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>`_ 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>