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52 lines
2.4 KiB
XML
52 lines
2.4 KiB
XML
<tool id="EMBOSS: tcode97" name="tcode" version="5.0.0">
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<description>Fickett TESTCODE statistic to identify protein-coding DNA</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>tcode -sequence '$input1' -outfile '$out_file1' -window '$window' -step '$step' -rformat '$out_format1' -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequence</label>
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</param>
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<param name="window" size="5" type="text" value="200">
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<label>Window size</label>
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</param>
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<param name="step" size="5" type="text" value="3">
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<label>Step size</label>
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</param>
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<param name="out_format1" type="select">
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<label>Output Report File Format</label>
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<option value="table">Table</option>
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<option value="embl">EMBL</option>
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<option value="genbank">GENBANK</option>
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<option value="gff">GFF</option>
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<option value="pir">PIR</option>
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<option value="swiss">SwissProt</option>
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<option value="dbmotif">DbMotif</option>
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<option value="diffseq">Diffseq</option>
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<option value="excel">Excel (tab delimited)</option>
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<option value="feattable">FeatTable</option>
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<option value="motif">Motif</option>
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<option value="regions">Regions</option>
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<option value="seqtable">SeqTable</option>
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<option value="simple">SRS Simple</option>
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<option value="srs">SRS</option>
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<option value="tagseq">TagSeq</option>
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</param>
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</inputs>
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<outputs>
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<data format="table" name="out_file1" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html
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------
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**Citation**
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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>`_
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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>`_
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</help>
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</tool> |