annotate rnasubopt.xml @ 3:292ae715791f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author rnateam
date Wed, 12 Jul 2017 14:28:33 -0400
parents 58fe85fe08be
children 685d5971df5b
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58fe85fe08be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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1 <tool id="viennarna_rnasubopt" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>Calculates suboptimal secondary structures of RNAs</description>
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3 <macros>
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4 <token name="@EXECUTABLE@">RNAsubopt</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 RNAsubopt < '$input' > '$output'
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13 -T$temperature
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14 --dangles=$dangling
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15 #if $methodOption.methodSelector == "range"
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16 --deltaEnergy=$methodOption.deltaenergy
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17 #else
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18 --stochBT=$methodOption.stochastic
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19 #end if
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20 #if $outputOption.outputSelector == "yes"
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21 --deltaEnergyPost=$deltaenergypost
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22 #end if
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23 $sorted
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24 $dos
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25 $zuker
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26 #if $varExists('$advancedOptions.nolp')
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27 $advancedOptions.noconversion
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28 $advancedOptions.nolp
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29 $advancedOptions.nogu
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30 $advancedOptions.noclosinggu
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31 $advancedOptions.notetra
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32 $advancedOptions.logml
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33 #end if
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34 #if $constraints.maxBPspan <> -1
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35 --maxBPspan=$constraints.maxBPspan
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36 #end if
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37 #if str($constraints.constraintLocation.constraintSelector) == "fromFile"
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38 --constraint='$constraints.constraintLocation.constraintsFile'
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39 $constraints.constraintLocation.canonicalBPonly
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40 $constraints.constraintLocation.enforceConstraint
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41 #end if
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42 #if str($constraints.shapeOption.shapeSelector) == "isUsed"
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43 --shape='$constraints.shapeOption.shapeFile'
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44 #if str($constraints.shapeOption.shapeMethod.methodSelector) == "W"
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45 #set $s="W"
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46 --shapeMethod=$s
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47 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z"
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48 #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b)
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49 --shapeMethod=$s
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50 #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"
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51 #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c)
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52 --shapeConversion=$c
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53 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L"
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54 #set $c="Ls"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
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55 --shapeConversion=$c
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56 #else if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O"
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57 #set $c="Os"+str($constraints.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($constraints.shapeOption.shapeMethod.shapeConversion.i)
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58 --shapeConversion=$c
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59 #else
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60 #set $c=str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector)
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61 --shapeConversion=$c
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62 #end if
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63 #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "D"
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64 #set $s="Dm"+str($constraints.shapeOption.shapeMethod.m)+"b"+str($constraints.shapeOption.shapeMethod.b)
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65 --shapeMethod=$s
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66 #end if
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67 #end if
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68 ]]>
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69 </command>
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70
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71 <inputs>
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72 <param format="fasta" name="input" type="data" label="Fasta file"/>
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73 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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74 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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75 <option value="2" selected="true">unpaired bases participate in all dangling ends (2)</option>
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76 <option value="0">ignore dangling ends (0)</option>
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77 <option value="1">unpaired bases participate in one dangling end only (1)</option>
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78 <option value="3">allow coaxial stacking (3)</option>
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79 </param>
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80
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81 <param name="sorted" type="boolean" truevalue="--sorted" falsevalue="" checked="false" label="Sort the secondary structures by energy" help="--sorted"/>
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82 <param name="dos" type="boolean" truevalue="--dos" falsevalue="" checked="false" label="Calculate the density of states instead of the structure" help="--dos"/>
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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"/>
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84
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85 <conditional name="methodOption">
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86 <param name="methodSelector" type="select" label="select algorithm">
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87 <option value="range" selected="true">energy range</option>
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88 <option value="stochastic">choose stochastically</option>
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89 </param>
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90 <when value="stochastic">
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91 <param name="stochastic" type="integer" value="1" label="Calculate this number of suboptimal structures chosen stochastically" help="--stochBT"/>
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92 </when>
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93 <when value="range">
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94 <param name="deltaenergy" type="float" optional="true" label="Range of energy for the suboptimal structures." help="--deltaEnergy"/>
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95 </when>
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96 </conditional>
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97
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98 <conditional name="outputOption">
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99 <param name="outputSelector" type="select" label="select output restriction">
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100 <option value="no" selected="true">no restriction</option>
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101 <option value="yes">restricted output</option>
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102 </param>
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103 <when value="no"/>
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104 <when value="yes">
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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"/>
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106 </when>
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107 </conditional>
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108
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109 <conditional name="advancedOptions">
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110 <param name="advancedSelector" type="select" label="advanced options">
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111 <option value="basic">basic Options</option>
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112 <option value="advanced">advanced Options</option>
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113 </param>
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114 <when value="advanced">
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115 <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
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116 <param name="nolp" type="boolean" truevalue="" falsevalue="--noLP" checked="true" label="Allow lonely base-pairs" help="(--noLP)"/>
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117 <param name="nogu" type="boolean" truevalue="" falsevalue="--noGU" checked="true" label="Allow GU pairing" help="--noGU"/>
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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"/>
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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)"/>
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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)"/>
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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"/>
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122 </when>
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123 <when value="basic">
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124 </when>
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125 </conditional>
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126
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127 <section name="constraints" title="Structure constraints">
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128 <param name="maxBPspan" type="integer" value="-1" label="Set the maximum base pair span" help="" argument="--maxBPspan"/>
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129 <conditional name="constraintLocation">
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130 <param name="constraintSelector" type="select" label="Constraints">
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131 <!-- <option value="fromInput">The constraints are included in the input file</option> -->
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132 <option value="fromFile">The constraints are in a seperate file</option>
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133 <option value="none" selected="true">Don't use constraints</option>
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134 </param>
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135 <!-- <when value="fromInput"></when> -->
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136 <when value="none"></when>
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137 <when value="fromFile">
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138 <param name="constraintsFile" type="data" format="*" label="Constraints file" argument="--constraint"/>
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139 <param argument="--canonicalBPonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Remove non-canonical base pairs from the structure constraint" />
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140 <param argument="--enforceConstraint" type="boolean" truevalue="--enforceConstraint" falsevalue="" checked="false" label="Enforce base pair given by round brackets () in structure constraint" />
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141 </when>
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142 </conditional>
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143
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144 <conditional name="shapeOption">
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145 <param name="shapeSelector" type="select" label="Shape reactivity data">
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146 <option value="isUsed">Use shape reactivity data</option>
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147 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
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148 </param>
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149 <when value ="isUsed">
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150 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/>
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151 <conditional name="shapeMethod">
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152 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
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153 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
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154 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
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155 <option value="W">W: Apply a given vector of perturbation energies to unpaired nucleotides according to Washietl et al 2012</option>
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156 </param>
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157 <when value="D">
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158 <param name="m" type="float" value="1.8" label="Slope m"/>
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159 <param name="b" type="float" value="-0.6" label="Intercept"/>
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160 </when>
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161 <when value="Z">
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162 <param name="b" type="float" value="-0.6" label="Intercept"/>
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163 <conditional name="shapeConversion">
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164 <param name="conversionSelector" type="select" label="shape reactivity data" argument="--shapeConversion">
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165 <option value="M">M: Use linear mapping according to Zarringhalam et al</option>
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166 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option>
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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>
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168 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option>
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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>
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170 </param>
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171 <when value="M">
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172 </when>
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173 <when value="C">
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174 <param name="c" type="float" value="0.25" label="Cutoff"/>
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175 </when>
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176 <when value="S">
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177 </when>
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178 <when value="L">
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179 <param name="s" type="float" value="0.68" label="Slope"/>
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180 <param name="i" type="float" value="0.2" label="Intercept"/>
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181 </when>
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182 <when value="O">
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183 <param name="s" type="float" value="1.6" label="Slope s"/>
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184 <param name="i" type="float" value="-2.29" label="Intercept"/>
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185 </when>
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186 </conditional>
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187 </when>
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188 <when value="W">
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189 </when>
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190 </conditional>
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191 </when>
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192 <when value="notUsed">
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193 </when>
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194 </conditional>
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195 </section>
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196 </inputs>
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197 <outputs>
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198 <data format="txt" name="output"/>
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199 </outputs>
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200 <tests>
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201 <test>
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202 <param name="input" value="rnasubopt_input1.fa"/>
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203 <output name="output" file="rnasubopt_result1.txt"/>
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204 </test>
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205 </tests>
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206 <help>
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207 <![CDATA[
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208
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209 **RNAsubopt**
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210
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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.
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212
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213 Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.
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214
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215
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216 -----
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217
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218 **Input format**
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219
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220 RNAsubopt requires one input file
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221
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222 - fasta file
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223
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224
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225 ------
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226
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227 **Outputs**
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228
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229 - secondary structure in dot-bracket format
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230
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231
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232 ]]>
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233 </help>
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234 <expand macro="citations" />
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235 </tool>