Mercurial > repos > xuebing > sharplabtool
comparison 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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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0"> | |
2 <!-- output contains file location info, commented out functional tests --> | |
3 <description>Find protein sequence regions with a biased composition</description> | |
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
5 <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command> | |
6 <inputs> | |
7 <param format="data" name="input1" type="data"> | |
8 <label>Sequences</label> | |
9 </param> | |
10 <param format="data" name="input2" type="data"> | |
11 <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> | |
12 </param> | |
13 <param name="window" size="4" type="text" value="30"> | |
14 <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> | |
15 </param> | |
16 <param name="ignorebz" type="select"> | |
17 <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 | |
18 containing them, just noting them in the count of 'Other' words</label> | |
19 <option value="yes">Yes</option> | |
20 <option value="no">No</option> | |
21 </param> | |
22 </inputs> | |
23 <outputs> | |
24 <data format="oddcomp" name="out_file1" /> | |
25 </outputs> | |
26 <!-- <tests> | |
27 <test> | |
28 <param name="input1" value="2.fasta"/> | |
29 <param name="input2" value="emboss_compseq_out.compseq"/> | |
30 <param name="window" value="30"/> | |
31 <param name="ignorebz" value="yes"/> | |
32 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/> | |
33 </test> | |
34 </tests> --> | |
35 <help> | |
36 You can view the original documentation here_. | |
37 | |
38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html | |
39 </help> | |
40 </tool> |