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42 lines
1.7 KiB
XML
42 lines
1.7 KiB
XML
<tool id="EMBOSS: cpgplot15" name="cpgplot">
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<description>Plot CpG rich areas</description>
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<command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -graph png -goutfile3 $out_file2
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-outfeat $out_file3 -offormat4 $out_format3 -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="text" value="100">
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<label>Window Size</label>
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</param>
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<param name="shift" size="4" type="text" value="1">
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<label>Step size (shift)</label>
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</param>
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<param name="minlen" size="4" type="text" 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="text" 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="text" 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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<param name="out_format3" type="select">
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<label>Output Feature File Format</label>
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<option value="gff">GFF</option>
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<option value="embl">EMBL</option>
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<option value="swiss">SwissProt</option>
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</param>
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</inputs>
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<outputs>
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<data format="txt" name="out_file1" />
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<data format="png" name="out_file2" />
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<data format="gff" name="out_file3" />
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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/4.0/emboss/apps/cpgplot.html
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</help>
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</tool> |