Mercurial > repos > rnateam > viennarna_rnasubopt
comparison rnasubopt.xml @ 0:58fe85fe08be 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 12:37:10 -0500 |
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children | 685d5971df5b |
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1 <tool id="viennarna_rnasubopt" name="@EXECUTABLE@" version="@VERSION@.0"> | |
2 <description>Calculates suboptimal secondary structures of RNAs</description> | |
3 <macros> | |
4 <token name="@EXECUTABLE@">RNAsubopt</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 RNAsubopt < '$input' > '$output' | |
13 -T$temperature | |
14 --dangles=$dangling | |
15 #if $methodOption.methodSelector == "range" | |
16 --deltaEnergy=$methodOption.deltaenergy | |
17 #else | |
18 --stochBT=$methodOption.stochastic | |
19 #end if | |
20 #if $outputOption.outputSelector == "yes" | |
21 --deltaEnergyPost=$deltaenergypost | |
22 #end if | |
23 $sorted | |
24 $dos | |
25 $zuker | |
26 #if $varExists('$advancedOptions.nolp') | |
27 $advancedOptions.noconversion | |
28 $advancedOptions.nolp | |
29 $advancedOptions.nogu | |
30 $advancedOptions.noclosinggu | |
31 $advancedOptions.notetra | |
32 $advancedOptions.logml | |
33 #end if | |
34 #if $constraints.maxBPspan <> -1 | |
35 --maxBPspan=$constraints.maxBPspan | |
36 #end if | |
37 #if str($constraints.constraintLocation.constraintSelector) == "fromFile" | |
38 --constraint='$constraints.constraintLocation.constraintsFile' | |
39 $constraints.constraintLocation.canonicalBPonly | |
40 $constraints.constraintLocation.enforceConstraint | |
41 #end if | |
42 #if str($constraints.shapeOption.shapeSelector) == "isUsed" | |
43 --shape='$constraints.shapeOption.shapeFile' | |
44 #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W" | |
45 #set $s="W" | |
46 --shapeMethod=$s | |
47 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z" | |
48 #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b) | |
49 --shapeMethod=$s | |
50 #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C" | |
51 #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c) | |
52 --shapeConversion=$c | |
53 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L" | |
54 #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i) | |
55 --shapeConversion=$c | |
56 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O" | |
57 #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i) | |
58 --shapeConversion=$c | |
59 #else | |
60 #set $c=str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) | |
61 --shapeConversion=$c | |
62 #end if | |
63 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "D" | |
64 #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b) | |
65 --shapeMethod=$s | |
66 #end if | |
67 #end if | |
68 ]]> | |
69 </command> | |
70 | |
71 <inputs> | |
72 <param format="fasta" name="input" type="data" label="Fasta file"/> | |
73 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/> | |
74 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d"> | |
75 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option> | |
76 <option value="0">ignore dangling ends (0)</option> | |
77 <option value="1">unpaired bases participate in one dangling end only (1)</option> | |
78 <option value="3">allow coaxial stacking (3)</option> | |
79 </param> | |
80 | |
81 <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/> | |
82 <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/> | |
83 <param name="zuker" type="boolean" truevalue="--zuker" falsevalue="" checked="false" label="Calculate the Zuker suboptimals instead of the structures within a range." help="--zuker"/> | |
84 | |
85 <conditional name="methodOption"> | |
86 <param name="methodSelector" type="select" label="select algorithm"> | |
87 <option value="range" selected="true">energy range</option> | |
88 <option value="stochastic">choose stochastically</option> | |
89 </param> | |
90 <when value="stochastic"> | |
91 <param name="stochastic" type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/> | |
92 </when> | |
93 <when value="range"> | |
94 <param name="deltaenergy" type="float" optional="true" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/> | |
95 </when> | |
96 </conditional> | |
97 | |
98 <conditional name="outputOption"> | |
99 <param name="outputSelector" type="select" label="select output restriction"> | |
100 <option value="no" selected="true">no restriction</option> | |
101 <option value="yes">restricted output</option> | |
102 </param> | |
103 <when value="no"/> | |
104 <when value="yes"> | |
105 <param name="deltaenergypost" type="float" value="0.0" label="Print only those structures that have a smaller difference in energy than the mfe." help="--deltaEnergyPost"/> | |
106 </when> | |
107 </conditional> | |
108 | |
109 <conditional name="advancedOptions"> | |
110 <param name="advancedSelector" type="select" label="advanced options"> | |
111 <option value="basic">basic Options</option> | |
112 <option value="advanced">advanced Options</option> | |
113 </param> | |
114 <when value="advanced"> | |
115 <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/> | |
116 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/> | |
117 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/> | |
118 <param name="noclosinggu" type="boolean" truevalue="" falsevalue="--noClosingGU" checked="true" label="Allow GU pairing at the ends" help="Allow pairing of G and U at the ends of helices. --noClosingGU"/> | |
119 <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)"/> | |
120 <param name="noconversion" type="boolean" truevalue="" falsevalue="--noconv" checked="true" label="Convert Thymine to Uracil (T -> U)" help="Avoids confusion with DNA sequences (--noconv)"/> | |
121 <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Recalculate energies of structures using a logarithmic energy function for multi-loops" help="--logML"/> | |
122 </when> | |
123 <when value="basic"> | |
124 </when> | |
125 </conditional> | |
126 | |
127 <section name="constraints" title="Structure constraints"> | |
128 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/> | |
129 <conditional name="constraintLocation"> | |
130 <param name="constraintSelector" type="select" label="Constraints"> | |
131 <!-- <option value="fromInput">The constraints are included in the input file</option> --> | |
132 <option value="fromFile">The constraints are in a seperate file</option> | |
133 <option value="none" selected="true">Don't use constraints</option> | |
134 </param> | |
135 <!-- <when value="fromInput"></when> --> | |
136 <when value="none"></when> | |
137 <when value="fromFile"> | |
138 <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/> | |
139 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from the structure constraint" /> | |
140 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" /> | |
141 </when> | |
142 </conditional> | |
143 | |
144 <conditional name="shapeOption"> | |
145 <param name="shapeSelector" type="select" label="Shape reactivity data"> | |
146 <option value="isUsed">Use shape reactivity data</option> | |
147 <option value="notUsed" selected="true">Don't use shape reactivity data</option> | |
148 </param> | |
149 <when value ="isUsed"> | |
150 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/> | |
151 <conditional name="shapeMethod"> | |
152 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod"> | |
153 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option> | |
154 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option> | |
155 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option> | |
156 </param> | |
157 <when value="D"> | |
158 <param name="m" type="float" value="1.8" label="Slope m"/> | |
159 <param name="b" type="float" value="-0.6" label="Intercept"/> | |
160 </when> | |
161 <when value="Z"> | |
162 <param name="b" type="float" value="-0.6" label="Intercept"/> | |
163 <conditional name="shapeConversion"> | |
164 <param name="conversionSelector" type="select" label="shape reactivity data" argument="--shapeConversion"> | |
165 <option value="M">M: Use linear mapping according to Zarringhalam et al</option> | |
166 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option> | |
167 <option value="S">S: Skip the normalizing step since the input data already represents probabilities for being unpaired rather than raw reactivity values</option> | |
168 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option> | |
169 <option value="O" selected="true">O: Use a linear model to convert the log of the reactivity into a probability for being unpaired</option> | |
170 </param> | |
171 <when value="M"> | |
172 </when> | |
173 <when value="C"> | |
174 <param name="c" type="float" value="0.25" label="Cutoff"/> | |
175 </when> | |
176 <when value="S"> | |
177 </when> | |
178 <when value="L"> | |
179 <param name="s" type="float" value="0.68" label="Slope"/> | |
180 <param name="i" type="float" value="0.2" label="Intercept"/> | |
181 </when> | |
182 <when value="O"> | |
183 <param name="s" type="float" value="1.6" label="Slope s"/> | |
184 <param name="i" type="float" value="-2.29" label="Intercept"/> | |
185 </when> | |
186 </conditional> | |
187 </when> | |
188 <when value="W"> | |
189 </when> | |
190 </conditional> | |
191 </when> | |
192 <when value="notUsed"> | |
193 </when> | |
194 </conditional> | |
195 </section> | |
196 </inputs> | |
197 <outputs> | |
198 <data format="txt" name="output"/> | |
199 </outputs> | |
200 <tests> | |
201 <test> | |
202 <param name="input" value="rnasubopt_input1.fa"/> | |
203 <output name="output" file="rnasubopt_result1.txt"/> | |
204 </test> | |
205 </tests> | |
206 <help> | |
207 <![CDATA[ | |
208 | |
209 **RNAsubopt** | |
210 | |
211 In the default -e mode RNAsubopt calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe). It prints the suboptimal structures in dot-bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range. | |
212 | |
213 Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures. | |
214 | |
215 | |
216 ----- | |
217 | |
218 **Input format** | |
219 | |
220 RNAsubopt requires one input file | |
221 | |
222 - fasta file | |
223 | |
224 | |
225 ------ | |
226 | |
227 **Outputs** | |
228 | |
229 - secondary structure in dot-bracket format | |
230 | |
231 | |
232 ]]> | |
233 </help> | |
234 <expand macro="citations" /> | |
235 </tool> |