Mercurial > repos > xuebing > sharplabtool
diff tools/emboss_5/emboss_oddcomp.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/emboss_5/emboss_oddcomp.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,40 @@ +<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0"> + <!-- output contains file location info, commented out functional tests --> + <description>Find protein sequence regions with a biased composition</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command> + <inputs> + <param format="data" name="input1" type="data"> + <label>Sequences</label> + </param> + <param format="data" name="input2" type="data"> + <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> + </param> + <param name="window" size="4" type="text" value="30"> + <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> + </param> + <param name="ignorebz" type="select"> + <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 + containing them, just noting them in the count of 'Other' words</label> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + </inputs> + <outputs> + <data format="oddcomp" name="out_file1" /> + </outputs> +<!-- <tests> + <test> + <param name="input1" value="2.fasta"/> + <param name="input2" value="emboss_compseq_out.compseq"/> + <param name="window" value="30"/> + <param name="ignorebz" value="yes"/> + <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/> + </test> + </tests> --> + <help> + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html + </help> +</tool> \ No newline at end of file