[2] | 1 | <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
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| 2 | <description>Report CpG rich areas</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
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| 5 | <inputs>
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| 6 | <param format="data" name="input1" type="data">
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| 7 | <label>Sequence</label>
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| 8 | </param>
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| 9 | <param name="window" size="4" type="text" value="100">
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| 10 | <label>Window Size</label>
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| 11 | </param>
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| 12 | <param name="shift" size="4" type="text" value="1">
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| 13 | <label>Step size (shift)</label>
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| 14 | </param>
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| 15 | <param name="minlen" size="4" type="text" value="200">
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| 16 | <label>Minimum length</label>
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| 17 | </param>
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| 18 | <param name="minoe" size="4" type="text" value="0.6">
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| 19 | <label>Minimum average observed to expected ratio</label>
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| 20 | </param>
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| 21 | <param name="minpc" size="4" type="text" value="50.0">
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| 22 | <label>Minimum average percentage of G plus C</label>
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| 23 | </param>
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| 24 | </inputs>
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| 25 | <outputs>
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| 26 | <data format="newcpgreport" name="out_file1" />
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| 27 | </outputs> |
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| 28 | <tests> |
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| 29 | <test> |
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| 30 | <param name="input1" value="2.fasta"/> |
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| 31 | <param name="window" value="100"/> |
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| 32 | <param name="shift" value="1"/> |
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| 33 | <param name="minlen" value="200"/> |
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| 34 | <param name="minoe" value="0.6"/> |
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| 35 | <param name="minpc" value="50.0"/> |
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| 36 | <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/> |
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| 37 | </test> |
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| 38 | </tests>
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| 39 | <help> |
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| 40 | You can view the original documentation here_. |
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| 41 | |
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| 42 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html |
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| 43 | </help> |
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| 44 | </tool> |
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