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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:12:41 -0500 |
parents | b94ca591877b |
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<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0"> <description>Reports all CpG rich regions</description> <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> <command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command> <inputs> <param format="fasta" name="input1" type="data"> <label>On query</label> </param> <param name="score" type="text" value="17"> <label>Score for each CG sequence found (1-200)</label> </param> <param name="out_format2" type="select"> <label>Output Feature File Format</label> <option value="gff">GFF</option> <option value="embl">EMBL</option> <option value="swiss">SwissProt</option> </param> </inputs> <outputs> <data format="cpgreport" name="out_file1" /> <data format="gff" name="out_file2" /> </outputs> <tests> <test> <param name="input1" value="2.fasta"/> <param name="score" value="17"/> <param name="out_format2" value="gff"/> <output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/> </test> <!-- <test> <param name="input1" value="2.fasta"/> <param name="score" value="17"/> <param name="out_format2" value="gff"/> <output name="out_file1" file="emboss_cpgreport_out1.gff"/> </test> --> </tests> <code file="emboss_format_corrector.py" /> <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/cpgreport.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>