/tools/emboss_5/emboss_wordcount.xml

 1<tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0">
 2  <description>Counts words of a specified size in a DNA sequence</description>
 3  <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command>
 4  <inputs>
 5    <param format="fasta" name="input1" type="data">
 6      <label>Sequence</label>
 7    </param>
 8    <param name="wordsize" size="5" type="text" value="4">
 9      <label>Word size</label>
10    </param>
11  </inputs>
12  <outputs>
13    <data format="wordcount" name="out_file1" />
14  </outputs>
15  <tests>
16    <test>
17      <param name="input1" value="2.fasta"/>
18      <param name="wordsize" value="4"/>
19      <output name="out_file1" file="emboss_wordcount_out.wordcount"/>
20    </test>
21  </tests>
22  <help>
23
24.. class:: warningmark 
25
26The input dataset needs to be sequences. 
27
28----- 
29
30    You can view the original documentation here_.
31    
32    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordcount.html
33  </help>
34</tool>