Mercurial > repos > devteam > emboss_5
comparison emboss_tcode.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: tcode97" name="tcode" version="5.0.0"> | |
| 2 <description>Fickett TESTCODE statistic to identify protein-coding DNA</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="data" name="input1" type="data"> | |
| 7 <label>Sequence</label> | |
| 8 </param> | |
| 9 <param name="window" type="text" value="200"> | |
| 10 <label>Window size</label> | |
| 11 </param> | |
| 12 <param name="step" type="text" value="3"> | |
| 13 <label>Step size</label> | |
| 14 </param> | |
| 15 <param name="out_format1" type="select"> | |
| 16 <label>Output Report File Format</label> | |
| 17 <option value="table">Table</option> | |
| 18 <option value="embl">EMBL</option> | |
| 19 <option value="genbank">GENBANK</option> | |
| 20 <option value="gff">GFF</option> | |
| 21 <option value="pir">PIR</option> | |
| 22 <option value="swiss">SwissProt</option> | |
| 23 <option value="dbmotif">DbMotif</option> | |
| 24 <option value="diffseq">Diffseq</option> | |
| 25 <option value="excel">Excel (tab delimited)</option> | |
| 26 <option value="feattable">FeatTable</option> | |
| 27 <option value="motif">Motif</option> | |
| 28 <option value="regions">Regions</option> | |
| 29 <option value="seqtable">SeqTable</option> | |
| 30 <option value="simple">SRS Simple</option> | |
| 31 <option value="srs">SRS</option> | |
| 32 <option value="tagseq">TagSeq</option> | |
| 33 </param> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="table" name="out_file1" /> | |
| 37 </outputs> | |
| 38 <code file="emboss_format_corrector.py" /> | |
| 39 <help> | |
| 40 You can view the original documentation here_. | |
| 41 | |
| 42 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html | |
| 43 | |
| 44 ------ | |
| 45 | |
| 46 **Citation** | |
| 47 | |
| 48 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>`_ | |
| 49 | |
| 50 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>`_ | |
| 51 </help> | |
| 52 </tool> |