|
0
|
1 <tool id="rnaalifold" name="RNAalifold" version="2.1.6.0">
|
|
|
2 <description>Calculate minimum free energy secondary structures and partition function on a multiple alignment file</description>
|
|
|
3 <expand macro="requirements" />
|
|
|
4 <expand macro="version_command" />
|
|
|
5 <expand macro="stdio" />
|
|
|
6 <macros>
|
|
|
7 <token name="@EXECUTABLE@">RNAalifold</token>
|
|
|
8 <import>macros.xml</import>
|
|
|
9 </macros>
|
|
|
10 <command>
|
|
|
11 <![CDATA[
|
|
|
12 RNAalifold < $input > $tabularFile
|
|
|
13 -T$temperature -d$dangling
|
|
|
14 $pf
|
|
|
15 $mis
|
|
|
16 #if $measelect.mea=="yes"
|
|
|
17 --mea=$measelect.meavalue
|
|
|
18 #end if
|
|
|
19 #if $backtrackselect.backtrack=="yes"
|
|
|
20 --stochBT_en=$backtrackselect.backtrackvalue
|
|
|
21 #end if
|
|
|
22 #if $varExists('$advancedOptions.color')
|
|
|
23 $advancedOptions.alignment
|
|
|
24 $advancedOptions.color
|
|
|
25 $advancedOptions.gquad
|
|
|
26 $advancedOptions.nolp
|
|
|
27 $advancedOptions.nogu
|
|
|
28 $advancedOptions.noclosinggu
|
|
|
29 $advancedOptions.notetra
|
|
|
30 $advancedOptions.canonicalonly
|
|
|
31 $advancedOptions.circular
|
|
|
32 --cfactor=$advancedOptions.cfactor
|
|
|
33 --nfactor=$advancedOptions.nfactor
|
|
|
34 $advancedOptions.endgaps
|
|
|
35 $advancedOptions.ribosum
|
|
|
36 #end if
|
|
|
37 ; tar -cf $imagesFile *.ps
|
|
|
38 ]]>
|
|
|
39 </command>
|
|
|
40 <inputs>
|
|
|
41 <param format="clustal" name="input" type="data" label="Clustal file"/>
|
|
|
42 <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
|
|
|
43 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
|
|
|
44 <option value="0">0: ignore dangling ends</option>
|
|
|
45 <option value="1">1: unpaired bases participate in one dangling end only</option>
|
|
|
46 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
|
|
|
47 <option value="3">3: allow coaxial stacking</option>
|
|
|
48 </param>
|
|
|
49 <param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>
|
|
|
50 <param name="mis" type="boolean" checked="false" truevalue="--mis" falsevalue="" label="Most Informative Sequence" help="--mis"/>
|
|
|
51 <conditional name="measelect">
|
|
|
52 <param name="mea" type="select" label="calculate maximum expected accuracy" help="--MEA">
|
|
|
53 <option value="no">no</option>
|
|
|
54 <option value="yes">yes</option>
|
|
|
55 </param>
|
|
|
56 <when value="yes">
|
|
|
57 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
|
|
|
58 </when>
|
|
|
59 </conditional>
|
|
|
60 <conditional name="backtrackselect">
|
|
|
61 <param name="backtrack" type="select" label="number of structures" help="--stochBT_en">
|
|
|
62 <option value="no">no</option>
|
|
|
63 <option value="yes">yes</option>
|
|
|
64 </param>
|
|
|
65 <when value="yes">
|
|
|
66 <param name="backtrackvalue" size="4" type="integer" value="1" label="Number of random structures."/>
|
|
|
67 </when>
|
|
|
68 </conditional>
|
|
|
69 <conditional name="advancedOptions">
|
|
|
70 <param name="advancedSelector" type="select" label="advanced options">
|
|
|
71 <option value="basic">basic Options</option>
|
|
|
72 <option value="advanced">advanced Options</option>
|
|
|
73 </param>
|
|
|
74 <when value="advanced">
|
|
|
75 <param name="alignment" type="boolean" truevalue="--aln" falsevalue="" checked="false" label="Colored and annotated alignment image" help="--color"/>
|
|
|
76 <param name="color" type="boolean" truevalue="--color" falsevalue="" checked="false" label="Colored secondary structure image" help="--color"/>
|
|
|
77 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
|
|
|
78 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
|
|
|
79 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/>
|
|
|
80 <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU don't allow pairing of G and U at the ends of helices."/>
|
|
|
81 <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
|
|
|
82 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
|
|
|
83 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
|
|
|
84 <param name="cfactor" size="6" type="float" value="1.0" label="Weight of the covariance term" help="--cfactor"/>
|
|
|
85 <param name="nfactor" size="6" type="float" value="1.0" label="Penalty for non-compatible sequences in the covariance term" help="--nfactor"/>
|
|
|
86 <param name="endgaps" type="boolean" truevalue="--endgaps" falsevalue="" checked="false" label="Score pairs with endgaps same as gap-gap pairs" help="--endgaps"/>
|
|
|
87 <param name="ribosum" type="boolean" truevalue="--ribosum_scoring" falsevalue="" checked="false" label="Use ribosum scoring matrix" help="--ribosum_scoring"/>
|
|
|
88 </when>
|
|
|
89 </conditional>
|
|
|
90 </inputs>
|
|
|
91 <outputs>
|
|
|
92 <data format="txt" name="tabularFile"/>
|
|
|
93 <data format="tar" name="imagesFile"/>
|
|
|
94 </outputs>
|
|
|
95 <tests>
|
|
2
|
96 <test>
|
|
|
97 <param name="input" value="rnaalifold_input1.clustal"/>
|
|
|
98 <output name="output" file="rnaalifold_result1.txt"/>
|
|
|
99 </test>
|
|
0
|
100 </tests>
|
|
|
101 <help>
|
|
|
102 <![CDATA[
|
|
|
103 **RNAalifold**
|
|
|
104
|
|
|
105 -----
|
|
|
106
|
|
|
107 **Input format**
|
|
|
108
|
|
|
109 RNAalifold requires one input file
|
|
|
110 - Clustal file
|
|
|
111
|
|
|
112 ------
|
|
|
113
|
|
|
114 **Outputs**
|
|
|
115
|
|
|
116 - energy of the consensus structures in the clustal file
|
|
|
117 - several possible postscript images bundled together in a tar file
|
|
|
118
|
|
|
119
|
|
|
120 ]]>
|
|
|
121 </help>
|
|
|
122 <expand macro="requirements" />
|
|
|
123 </tool>
|
