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48 lines
2.6 KiB
XML
48 lines
2.6 KiB
XML
<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
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<!-- output contains file location info, commented out functional tests -->
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<description>Find protein sequence regions with a biased composition</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window '$window' -ignorebz '$ignorebz' -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param format="data" name="input2" type="data">
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<label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
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</param>
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<param name="window" size="4" type="text" value="30">
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<label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
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</param>
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<param name="ignorebz" type="select">
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<label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words
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containing them, just noting them in the count of 'Other' words</label>
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<option value="yes">Yes</option>
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<option value="no">No</option>
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</param>
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</inputs>
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<outputs>
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<data format="oddcomp" name="out_file1" />
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</outputs>
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<!-- <tests>
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<test>
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<param name="input1" value="2.fasta"/>
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<param name="input2" value="emboss_compseq_out.compseq"/>
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<param name="window" value="30"/>
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<param name="ignorebz" value="yes"/>
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<output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
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</test>
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</tests> -->
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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/oddcomp.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> |