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/tools/emboss_5/emboss_oddcomp.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central
XML | 39 lines | 28 code | 1 blank | 10 comment | 0 complexity | 88db690752459224d82eed574880d574 MD5 | raw file
 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  <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
 5  <inputs>
 6    <param format="data" name="input1" type="data">
 7      <label>Sequences</label>
 8    </param>
 9    <param format="data" name="input2" type="data">
10      <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>
11    </param>
12    <param name="window" size="4" type="text" value="30">
13      <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>
14    </param>
15    <param name="ignorebz" type="select">
16      <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
17      containing them, just noting them in the count of 'Other' words</label>
18      <option value="yes">Yes</option>
19      <option value="no">No</option>
20    </param>
21  </inputs>
22  <outputs>
23    <data format="oddcomp" name="out_file1" />
24  </outputs>
25<!--    <tests>
26    <test>
27      <param name="input1" value="2.fasta"/>
28      <param name="input2" value="emboss_compseq_out.compseq"/>
29      <param name="window" value="30"/>
30      <param name="ignorebz" value="yes"/>
31      <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
32    </test>
33  </tests> -->
34  <help>
35    You can view the original documentation here_.
36    
37    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html
38  </help>
39</tool>