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29 lines
1.5 KiB
XML
29 lines
1.5 KiB
XML
<tool id="EMBOSS: oddcomp64" name="oddcomp">
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<description>Find protein sequence regions with a biased composition</description>
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<command>oddcomp -sequence $input1 -compdatafile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param format="data" name="input2" type="data">
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<label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
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</param>
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<param name="window" size="4" type="text" value="30">
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<label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
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</param>
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<param name="ignorebz" type="select">
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<label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words
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containing them, just noting them in the count of 'Other' words</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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</inputs>
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<outputs>
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<data format="txt" name="out_file1" />
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</outputs>
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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/oddcomp.html
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</help>
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</tool> |