/tools/emboss_5/emboss_compseq.xml

 1<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
 2  <description>Count composition of dimer/trimer/etc words in a sequence</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>On query</label>
 8    </param>
 9    <param name="word" size="4" type="text" value="2">
10      <label>Size of word (window) to count</label>
11    </param>
12    <param name="frame" type="select">
13      <label>Frame to inspect</label>
14      <option value="0">All Frames</option>
15      <option value="1">Frame 1</option>
16      <option value="2">Frame 2</option>
17      <option value="3">Frame 3</option>
18    </param>
19  </inputs>
20  <outputs>
21    <data format="compseq" name="out_file1" />
22  </outputs>
23  <tests>
24    <test>
25      <param name="input1" value="2.fasta"/>
26      <param name="word" value="2"/>
27      <param name="frame" value="0"/>
28      <output name="out_file1" file="emboss_compseq_out.compseq"/>
29    </test>
30  </tests>
31  <help>
32.. class:: warningmark
33
34The input dataset needs to be sequences.
35
36-----
37
38    You can view the original documentation here_.
39    
40    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html
41
42------
43
44**Citation**
45
46If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
47  </help>
48</tool>