/tools/emboss_5/emboss_wordmatch.xml

 1<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
 2  <description>Finds all exact matches of a given size between 2 sequences</description>
 3  <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
 4  -offormat5 $out_format3 -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequence 1</label>
 8    </param>
 9    <param format="fasta" name="input2" type="data">
10      <label>Sequence 2</label>
11    </param>
12    <param name="wordsize" size="5" type="text" value="4">
13      <label>Word size</label>
14    </param>
15    <param name="out_format1" type="select">
16      <label>Output Alignment File Format</label>
17      <option value="match">Match (m)</option>
18      <option value="simple">Simple (m)</option>
19      <option value="fasta">FASTA (m)</option>
20      <option value="msf">MSF (m)</option>
21      <option value="srs">SRS (m)</option>
22      <option value="pair">Pair (p)</option>
23      <option value="markx0">Markx0 (p)</option>
24      <option value="markx1">Markx1 (p)</option>
25      <option value="markx2">Markx2 (p)</option>
26      <option value="markx3">Markx3 (p)</option>
27      <option value="markx10">Markx10 (p)</option>
28      <option value="srspair">SRS pair (p)</option>
29      <option value="score">Score (p)</option>
30    </param>
31    <param name="out_format2" type="select">
32      <label>Output Feature 1 File Format</label>
33      <option value="gff">GFF</option>
34      <option value="embl">EMBL</option>
35      <option value="swiss">SwissProt</option>
36    </param>
37    <param name="out_format3" type="select">
38      <label>Output Feature 2 File Format</label>
39      <option value="gff">GFF</option>
40      <option value="embl">EMBL</option>
41      <option value="swiss">SwissProt</option>
42    </param>
43  </inputs>
44  <outputs>
45    <data format="match" name="out_file1" />
46    <data format="gff" name="out_file2" />
47    <data format="gff" name="out_file3" />
48  </outputs>
49  <!--   <tests>
50    <test>
51      <param name="input1" value="2.fasta"/>
52      <param name="input2" value="1.fasta"/>
53      <param name="wordsize" value="4"/>
54      <param name="out_format1" value="fasta"/>
55      <param name="out_format2" value="gff"/>
56      <param name="out_format3" value="gff"/>
57      <output name="ofile2" file="emboss_wordmatch_out.embl"/>
58    </test> 
59  </tests> test takes a long time to run-->
60  <code file="emboss_format_corrector.py" />
61  <help>
62
63.. class:: warningmark 
64
65The input datasets need to be sequences. 
66
67----- 
68
69    You can view the original documentation here_.
70    
71    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
72  </help>
73</tool>