Mercurial > repos > rnateam > viennarna_rnaeval
comparison rnaeval.xml @ 0:4d59d9c739a5 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
author | rnateam |
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date | Tue, 06 Dec 2016 12:32:16 -0500 |
parents | |
children | a3934747a65f |
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-1:000000000000 | 0:4d59d9c739a5 |
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1 <tool id="viennarna_rnaeval" name="@EXECUTABLE@" version="@VERSION@.0"> | |
2 <description>Calculate energy of RNA sequences with given secondary structure</description> | |
3 <macros> | |
4 <token name="@EXECUTABLE@">RNAeval</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <expand macro="stdio" /> | |
9 <expand macro="version_command" /> | |
10 <command> | |
11 <![CDATA[ | |
12 RNAeval < '$input' > '$tabularFile' | |
13 -T$temperature -d$dangling | |
14 #if $varExists('$advancedOptions.noconversion') | |
15 $advancedOptions.noconversion | |
16 $advancedOptions.verbose | |
17 $advancedOptions.gquad | |
18 $advancedOptions.circ | |
19 $advancedOptions.logml | |
20 $advancedOptions.notetra | |
21 #if str($advancedOptions.shapeOption.shapeSelector) == "isUsed" | |
22 --shape='$advancedOptions.shapeOption.shapeFile' | |
23 #if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "W" | |
24 #set $s="W" | |
25 --shapeMethod=$s | |
26 #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "Z" | |
27 #set $s="Zb"+str($advancedOptions.shapeOption.shapeMethod.b) | |
28 --shapeMethod=$s | |
29 #if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C" | |
30 #set $c="C"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.c) | |
31 --shapeConversion=$c | |
32 #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L" | |
33 #set $c="Ls"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i) | |
34 --shapeConversion=$c | |
35 #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O" | |
36 #set $c="Os"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i) | |
37 --shapeConversion=$c | |
38 #else | |
39 #set $c=str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) | |
40 --shapeConversion=$c | |
41 #end if | |
42 #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "D" | |
43 #set $s="Dm"+str($advancedOptions.shapeOption.shapeMethod.m)+"b"+str($advancedOptions.shapeOption.shapeMethod.b) | |
44 --shapeMethod=$s | |
45 #end if | |
46 #end if | |
47 #end if | |
48 ]]> | |
49 </command> | |
50 <inputs> | |
51 <param format="txt,dbn" name="input" type="data" label="Input file"/> | |
52 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/> | |
53 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> | |
54 <option value="0">0: ignore dangling ends</option> | |
55 <option value="1">1: unpaired bases participate in one dangling end only</option> | |
56 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option> | |
57 <option value="3">3: allow coaxial stacking</option> | |
58 </param> | |
59 <conditional name="advancedOptions"> | |
60 <param name="advancedSelector" type="select" label="advanced options"> | |
61 <option value="basic">basic Options</option> | |
62 <option value="advanced">advanced Options</option> | |
63 </param> | |
64 <when value="advanced"> | |
65 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Print out energy of each loop in the structure." help="--verbose"/> | |
66 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G-quadruplex formation prediction" help="--gquad"/> | |
67 <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA" help="--circ"/> | |
68 <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops" help="--logML"/> | |
69 <param name="notetra" type="boolean" truevalue="" falsevalue="--noTetra" checked="true" label="Allow stabilization for loops, hairpins etc." help=" Include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing. (--noTetra)"/> | |
70 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> | |
71 <conditional name="shapeOption"> | |
72 <param name="shapeSelector" type="select" label="Shape reactivity data"> | |
73 <option value="isUsed">Use shape reactivity data</option> | |
74 <option value="notUsed" selected="true">Don't use shape reactivity data</option> | |
75 </param> | |
76 <when value ="isUsed"> | |
77 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/> | |
78 <conditional name="shapeMethod"> | |
79 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> | |
80 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> | |
81 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option> | |
82 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option> | |
83 </param> | |
84 <when value="D"> | |
85 <param name="m" type="float" value="1.8" label="Slope m"/> | |
86 <param name="b" type="float" value="-0.6" label="Intercept"/> | |
87 </when> | |
88 <when value="Z"> | |
89 <param name="b" type="float" value="-0.6" label="Intercept"/> | |
90 <conditional name="shapeConversion"> | |
91 <param name="conversionSelector" type="select" label="shape reactivity data"> | |
92 <option value="M">M: Use linear mapping according to Zarringhalam et al</option> | |
93 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option> | |
94 <option value="S">S: Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values</option> | |
95 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option> | |
96 <option value="O" selected="true">O: Use a linear model to convert the log of the reactivity into a probability for being unpaired</option> | |
97 </param> | |
98 <when value="M"> | |
99 </when> | |
100 <when value="C"> | |
101 <param name="c" type="float" value="0.25" label="Cutoff"/> | |
102 </when> | |
103 <when value="S"> | |
104 </when> | |
105 <when value="L"> | |
106 <param name="s" type="float" value="0.68" label="Slope"/> | |
107 <param name="i" type="float" value="0.2" label="Intercept"/> | |
108 </when> | |
109 <when value="O"> | |
110 <param name="s" type="float" value="1.6" label="Slope s"/> | |
111 <param name="i" type="float" value="-2.29" label="Intercept"/> | |
112 </when> | |
113 </conditional> | |
114 </when> | |
115 <when value="W"> | |
116 </when> | |
117 </conditional> | |
118 </when> | |
119 <when value="notUsed"> | |
120 </when> | |
121 </conditional> | |
122 </when> | |
123 <when value="basic"> | |
124 </when> | |
125 </conditional> | |
126 </inputs> | |
127 <outputs> | |
128 <data format="txt" name="tabularFile"/> | |
129 </outputs> | |
130 <tests> | |
131 <test> | |
132 <param name="input" value="rnaeval_input1.dbn"/> | |
133 <output name="out_file" file="rnaeval_result1.txt"/> | |
134 </test> | |
135 </tests> | |
136 <help> | |
137 <![CDATA[ | |
138 **RNAeval** | |
139 RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure. Sequences and structures are read alternately from stdin. The energy in Kcal/Mol is written to stdout. | |
140 | |
141 ----- | |
142 | |
143 **Input format** | |
144 | |
145 RNAeval requires one input file in a format similar to the Fasta format. The secondary strucures should be added after the sequence in dot-bracket notation. Sequence and structure can be interupted by an '&' to calculate the co-folding of two RNA-strands. | |
146 | |
147 | |
148 ------ | |
149 | |
150 **Outputs** | |
151 | |
152 First line: the sequence, second line: the structure with its corresponding energy | |
153 | |
154 | |
155 ]]> | |
156 </help> | |
157 <expand macro="citations" /> | |
158 </tool> |