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41 lines
2.0 KiB
XML
41 lines
2.0 KiB
XML
<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
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<description>Plot CpG rich areas</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence '$input1' -window '$window' -minlen '$minlen' -minpc '$minpc' -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe '$minoe' -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="window" size="4" type="integer" value="100">
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<label>Window Size</label>
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</param>
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<param name="minlen" size="4" type="integer" value="200">
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<label>Minimum length</label>
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</param>
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<param name="minoe" size="4" type="float" value="0.6">
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<label>Minimum average observed to expected ratio</label>
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</param>
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<param name="minpc" size="4" type="float" value="50.0">
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<label>Minimum average percentage of G plus C</label>
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</param>
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</inputs>
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<outputs>
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<data format="cpgplot" name="outfile" />
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<data format="png" name="goutfile" />
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<data format="gff" name="outfeat" />
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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/cpgplot.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> |