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57 lines
2.3 KiB
XML
57 lines
2.3 KiB
XML
<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0">
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<!-- produces png file, not added functional tests -->
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<description>Displays all-against-all dotplots of a set of sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize '$wordsize' -boxit '$boxit' -dumpfeat yes -gap
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'$gap' -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Sequence</label>
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</param>
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<param name="wordsize" size="10" type="text" value="6">
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<label>Word size</label>
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</param>
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<param name="boxit" type="select">
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<label>Draw a box around each dotplot</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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<param name="gap" size="10" type="text" value="10">
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<label>Size of gap</label>
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</param>
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</inputs>
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<outputs>
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<data format="polydot" name="output1" />
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<data format="png" name="output2" />
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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="wordsize" value="6"/>
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<param name="boxit" value="yes"/>
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<param name="gap" value="10"/>
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<output name="output1" file="emboss_polydot_out.png"/>
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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/polydot.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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