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51 lines
2.0 KiB
XML
51 lines
2.0 KiB
XML
<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
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<description>Count composition of dimer/trimer/etc words in a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>compseq -sequence '$input1' -outfile '$out_file1' -word '$word' -frame '$frame' -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>On query</label>
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</param>
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<param name="word" size="4" type="text" value="2">
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<label>Size of word (window) to count</label>
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</param>
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<param name="frame" type="select">
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<label>Frame to inspect</label>
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<option value="0">All Frames</option>
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<option value="1">Frame 1</option>
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<option value="2">Frame 2</option>
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<option value="3">Frame 3</option>
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</param>
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</inputs>
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<outputs>
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<data format="compseq" 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="word" value="2"/>
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<param name="frame" value="0"/>
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<output name="out_file1" file="emboss_compseq_out.compseq"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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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/compseq.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>
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