/tools/emboss_5/emboss_pepcoil.xml

 1<tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
 2  <description>Predicts coiled coil regions</description>
 3  <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
 4  <inputs>
 5    <param format="data" name="input1" type="data">
 6      <label>Sequence</label>
 7    </param>
 8    <param name="window" size="4" type="text" value="28">
 9      <label>Window size</label>
10    </param>
11    <param name="coil" type="select">
12      <label>Report coiled coil regions</label>
13      <option value="yes">Yes</option>
14      <option value="no">No</option>
15    </param>
16    <param name="frame" type="select">
17      <label>Show coil frameshifts</label>
18      <option value="yes">Yes</option>
19      <option value="no">No</option>
20    </param>
21    <param name="other" type="select">
22      <label>Report non coiled coil regions</label>
23      <option value="yes">Yes</option>
24      <option value="no">No</option>
25    </param>
26  </inputs>
27  <outputs>
28    <data format="pepcoil" name="out_file1" />
29  </outputs>
30  <tests>
31    <test>
32      <param name="input1" value="2.fasta"/>
33      <param name="window" value="28"/>
34      <param name="coil" value="yes"/>
35      <param name="frame" value="yes"/>
36      <param name="other" value="yes"/>
37      <output name="out_file1" file="emboss_pepcoil_out.pepcoil"/>
38    </test>
39  </tests>
40  <help>
41    You can view the original documentation here_.
42    
43    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html
44  </help>
45</tool>