Mercurial > repos > pdeford > dotplot
view dotplot/dotplot.xml @ 0:a8fcdd1c2cce draft
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author | pdeford |
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date | Tue, 01 Nov 2016 15:19:49 -0400 |
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children | 9642674cbe9b |
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<tool id="lastz_dotplot_matplotlib" name="Dot Plot" version="1.0.0"> <description>of LASTZ tabular output</description> <requirements> <requirement type="package">numpy</requirement> <requirement type="package">matplotlib</requirement> </requirements> <command interpreter="python">dotplot.py $input $filter $outfile1</command> <inputs> <param name="input" type="data" format="tabular" label="LASTZ tabular output" help="Dataset missing? See TIP below"/> <param name="filter" type="text" value="0" label="Filter out alignments shorter than (bp)"/> </inputs> <outputs> <data format="pdf" name="out_file1"/> </outputs> <tests> <test> <param name="input" value="human_vs_chicken_chr4.tabular" ftype="tabular"/> <param name="filter" value="100"/> <output name="out_file1" file="dotplot_chr4.pdf" compare="sim_size" /> </test> </tests> <help> **Syntax** This tool creates a dot plot of the contents of a LASTZ tabular file resulting from the alignment of one or more sequences to a single reference sequence. If multiple query sequences are present, they will be sorted by size, offset from one another in the dot plot, and separated by a gray line. - **filter** all alignments shorter than the filter will be excluded from the analysis. ----- **Example** Chicken chromosome 4 was aligned against human chromosome 4 using LASTZ, specifying tabular output, no transitions, and performing gap free extension. Using a 100 bp filter above we get the following dotplot. .. image:: dotplot_chr4.png </help> </tool>