/tools/emboss_5/emboss_einverted.xml

 1<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
 2  <description>Finds DNA inverted repeats</description>
 3  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
 4  <inputs>
 5    <param format="fasta" name="input1" type="data">
 6      <label>On query</label>
 7    </param>
 8    <param name="gap" size="4" type="text" value="12">
 9      <label>Gap penalty</label>
10    </param>
11    <param name="threshold" size="4" type="text" value="50">
12      <label>Minimum score threshold</label>
13    </param>
14    <param name="match" size="4" type="text" value="3">
15      <label>Match score</label>
16    </param>
17    <param name="mismatch" size="4" type="text" value="-4">
18      <label>Mismatch score</label>
19    </param>
20    <param name="maxrepeat" size="4" type="text" value="2000">
21      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
22    </param>
23  </inputs>
24  <outputs>
25    <data format="einverted" name="out_file1" />
26  </outputs>
27  <tests>
28    <test>
29      <param name="input1" value="1.fasta"/>
30      <param name="gap" value="12"/>
31      <param name="threshold" value="50"/>
32      <param name="match" value="3"/>
33      <param name="mismatch" value="-4"/>
34      <param name="maxrepeat" value="2000"/>
35      <output name="out_file1" file="emboss_einverted_out.einverted"/>
36    </test>
37  </tests>
38  <help>
39.. class:: warningmark
40
41The input dataset needs to be sequences.
42
43-----
44
45    You can view the original documentation here_.
46    
47    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
48  </help>
49</tool>