|
2
|
1 <tool id="EMBOSS: krnafold" name="krnafold" version="1.0.2">
|
|
|
2 <description>Predicts secondary structure of single starnd RNA or DNA using RNAfold</description>
|
|
|
3 <command>krnafold -seqall $input1 -noclosegu $noclosegu -nolp $nolp -dangling $dangling -param $param -tmp $tmp -circ $circ -auto -outfile $out_file1</command>
|
|
|
4 <inputs>
|
|
|
5 <param format="data" name="input1" type="data">
|
|
|
6 <label>Sequence</label>
|
|
|
7 </param>
|
|
|
8 <param name="noclosegu" type="select" value="no">
|
|
|
9 <label>no GU pairs at the end of helices</label>
|
|
|
10 <option value="no">No</option>
|
|
|
11 <option value="yes">Yes</option>
|
|
|
12 </param>
|
|
|
13 <param name="nolp" type="select" value="yes">
|
|
|
14 <label>avoid isolated base pairs</label>
|
|
|
15 <option value="no">No</option>
|
|
|
16 <option value="yes">Yes</option>
|
|
|
17 </param>
|
|
|
18 <param name="dangling" size="4" type="text" value="d2">
|
|
|
19 <label>Dangling end options</label>
|
|
|
20 </param>
|
|
|
21 <param name="param" size="4" type="text" value="rna">
|
|
|
22 <label>Energy Parameters</label>
|
|
|
23 </param>
|
|
|
24 <param name="tmp" size="4" type="integer" value="37">
|
|
|
25 <label>rescale energy parameters to given temperature (C)</label>
|
|
|
26 </param>
|
|
|
27 <param name="circ" type="select" value="no">
|
|
|
28 <label>assume RNA molecule to be circular</label>
|
|
|
29 <option value="no">No</option>
|
|
|
30 <option value="yes">Yes</option>
|
|
|
31 </param>
|
|
|
32
|
|
|
33 </inputs>
|
|
|
34 <outputs>
|
|
|
35 <data format="txt" name="out_file1" label="${tool.name} for ${input1.name}" />
|
|
|
36 </outputs>
|
|
|
37 </tool>
|
