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comparison rnafold.xml @ 0:031ad3250176 draft

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author rnateam
date Tue, 03 Feb 2015 04:59:51 -0500
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1 <tool id="rnafold" name="RNAfold" version="2.1.6.0">
2 <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <expand macro="stdio" />
6 <macros>
7 <token name="@EXECUTABLE@">RNAfold</token>
8 <import>macros.xml</import>
9 </macros>
10 <command>
11 <![CDATA[
12 RNAfold
13 -T $temperature
14 --dangles=$dangling
15 #if $measelect.mea == "yes":
16 --MEA=$measelect.meavalue
17 #else
18 $measelect.pf
19 #end if
20 #if $varExists('$advancedOptions.nogu'):
21 $advancedOptions.noconversion
22 $advancedOptions.gquad
23 $advancedOptions.nolp
24 $advancedOptions.nogu
25 $advancedOptions.noclosinggu
26 $advancedOptions.canonicalonly
27 $advancedOptions.circular
28 #end if
29
30 < $fasta_input
31
32 > $tabular_file
33 ]]>
34 </command>
35
36 <inputs>
37 <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
38 <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
39 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
40 <option value="0">0: ignore dangling ends</option>
41 <option value="1">1: unpaired bases participate in one dangling end only</option>
42 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
43 <option value="3">3: allow coaxial stacking</option>
44 </param>
45 <conditional name="measelect">
46 <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
47 <option value="no">No</option>
48 <option value="yes">Yes</option>
49 </param>
50 <when value="yes">
51 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
52 </when>
53 <when value="no">
54 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
55 </when>
56 </conditional>
57 <conditional name="advancedOptions">
58 <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
59 <when value="true">
60 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv do not convert thymine to uracile (T -> U)."/>
61 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g take into account G Quadruplex formation"/>
62 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP don't allow lonely pairs."/>
63 <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU don't allow pairing of G and U."/> <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."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
64 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
65 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
66 </when>
67 </conditional>
68 </inputs>
69 <outputs>
70 <data format="tabular" name="tabular_file"/>
71 <data format="txt" name="structure">
72 <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" visible="true"/>
73 </data>
74 <data format="txt" name="dotplot">
75 <filter>measelect['pf'] is True</filter>
76 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
77 </data>
78 </outputs>
79 <tests>
80 </tests>
81 <help>
82 <![CDATA[
83 **RNAfold**
84
85 The program reads RNA sequences, calculates their minimum free
86 energy (mfe) structure and the mfe structure in dot-bracket notation.
87
88 If the -p option was given it also computes the
89 partition function (pf) and base pairing probability matrix.
90
91 The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing
92 probability in the upper right half, and one square for each pair in the
93 minimum free energy structure in the lower left half. For each pair i-j with
94 probability p>10E-6 there is a line of the form
95
96 i j sqrt(p) ubox
97
98 in the PostScript file, so that the pair probabilities can be easily extracted.
99
100 The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively.
101 The program will read the whole FASTA input file and provide output for each found sequence.
102
103
104 -----
105
106 **Input format**
107
108 RNAfold requires one input file
109 - FASTA file
110
111 ------
112
113 **Outputs**
114
115 - Secondary structures in dot-bracket notation
116
117 - several possible postscript images bundled together in a tar file
118 - secondary structure for each sequence in the input file
119 - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence
120
121 ]]>
122 </help>
123 <expand macro="citations" />
124 </tool>