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comparison emboss_oddcomp.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1">
2 <!-- output contains file location info, commented out functional tests -->
3 <description>Find protein sequence regions with a biased composition</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="data" label="Sequences" />
11 <param name="input2" type="data" format="data" label="Dataset in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis" />
12 <param name="window" type="integer" value="30" label="Size of window in which to count" help="If you want to count frequencies in a 40 aa stretch you should enter 40 here" />
13 <param name="ignorebz" type="select" label="Ignore B and Z" help="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">
14 <option value="yes">Yes</option>
15 <option value="no">No</option>
16 </param>
17 </inputs>
18 <outputs>
19 <data name="out_file1" format="oddcomp" />
20 </outputs>
21 <!-- <tests>
22 <test>
23 <param name="input1" value="2.fasta"/>
24 <param name="input2" value="emboss_compseq_out.compseq"/>
25 <param name="window" value="30"/>
26 <param name="ignorebz" value="yes"/>
27 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
28 </test>
29 </tests> -->
30 <help>
31 You can view the original documentation here_.
32
33 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/oddcomp.html
34 </help>
35 <expand macro="citations" />
36 </tool>