annotate 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
date Tue, 06 Dec 2016 12:32:16 -0500
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4d59d9c739a5 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_rnaeval" name="@EXECUTABLE@" version="@VERSION@.0">
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2 <description>Calculate energy of RNA sequences with given secondary structure</description>
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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3 <macros>
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4 <token name="@EXECUTABLE@">RNAeval</token>
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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5 <import>macros.xml</import>
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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6 </macros>
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7 <expand macro="requirements" />
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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8 <expand macro="stdio" />
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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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 RNAeval < '$input' > '$tabularFile'
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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13 -T$temperature -d$dangling
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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14 #if $varExists('$advancedOptions.noconversion')
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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15 $advancedOptions.noconversion
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16 $advancedOptions.verbose
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17 $advancedOptions.gquad
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18 $advancedOptions.circ
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19 $advancedOptions.logml
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20 $advancedOptions.notetra
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21 #if str($advancedOptions.shapeOption.shapeSelector) == "isUsed"
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22 --shape='$advancedOptions.shapeOption.shapeFile'
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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23 #if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "W"
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24 #set $s="W"
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25 --shapeMethod=$s
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26 #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "Z"
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27 #set $s="Zb"+str($advancedOptions.shapeOption.shapeMethod.b)
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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28 --shapeMethod=$s
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29 #if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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30 #set $c="C"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.c)
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31 --shapeConversion=$c
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32 #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "L"
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33 #set $c="Ls"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i)
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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34 --shapeConversion=$c
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35 #else if str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "O"
4d59d9c739a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 0065dafe7bbd382bb995b28cc4089c9e4f4eeeb9
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36 #set $c="Os"+str($advancedOptions.shapeOption.shapeMethod.shapeConversion.s)+"i"+ str($advancedOptions.shapeOption.shapeMethod.shapeConversion.i)
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37 --shapeConversion=$c
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38 #else
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39 #set $c=str($advancedOptions.shapeOption.shapeMethod.shapeConversion.conversionSelector)
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40 --shapeConversion=$c
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41 #end if
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42 #else if str($advancedOptions.shapeOption.shapeMethod.methodSelector) == "D"
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43 #set $s="Dm"+str($advancedOptions.shapeOption.shapeMethod.m)+"b"+str($advancedOptions.shapeOption.shapeMethod.b)
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44 --shapeMethod=$s
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45 #end if
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46 #end if
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47 #end if
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48 ]]>
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49 </command>
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50 <inputs>
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51 <param format="txt,dbn" name="input" type="data" label="Input file"/>
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52 <param name="temperature" type="float" value="37.0" label="temperature [°C]" help="-T"/>
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53 <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
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54 <option value="0">0: ignore dangling ends</option>
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55 <option value="1">1: unpaired bases participate in one dangling end only</option>
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56 <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
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57 <option value="3">3: allow coaxial stacking</option>
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58 </param>
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59 <conditional name="advancedOptions">
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60 <param name="advancedSelector" type="select" label="advanced options">
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61 <option value="basic">basic Options</option>
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62 <option value="advanced">advanced Options</option>
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63 </param>
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64 <when value="advanced">
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65 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Print out energy of each loop in the structure." help="--verbose"/>
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66 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G-quadruplex formation prediction" help="--gquad"/>
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67 <param name="circ" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA" help="--circ"/>
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68 <param name="logml" type="boolean" truevalue="--logML" falsevalue="" checked="false" label="Logarithmic energy functions for multi-loops" help="--logML"/>
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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)"/>
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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)"/>
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71 <conditional name="shapeOption">
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72 <param name="shapeSelector" type="select" label="Shape reactivity data">
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73 <option value="isUsed">Use shape reactivity data</option>
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74 <option value="notUsed" selected="true">Don't use shape reactivity data</option>
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75 </param>
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76 <when value ="isUsed">
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77 <param type="data" name="shapeFile" format="shape,*" label="Shape file" argument="--shape"/>
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78 <conditional name="shapeMethod">
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79 <param name="methodSelector" type="select" label="Shape reactivity data" argument="--shapeMethod">
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80 <option value="D" selected="true">D: Convert by using a linear equation according to Deigan et al 2009</option>
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81 <option value="Z">Z: Convert SHAPE reactivities to pseudo energies according to Zarringhalam et al 2012.</option>
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82 <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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83 </param>
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84 <when value="D">
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85 <param name="m" type="float" value="1.8" label="Slope m"/>
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86 <param name="b" type="float" value="-0.6" label="Intercept"/>
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87 </when>
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88 <when value="Z">
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89 <param name="b" type="float" value="-0.6" label="Intercept"/>
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90 <conditional name="shapeConversion">
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91 <param name="conversionSelector" type="select" label="shape reactivity data">
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92 <option value="M">M: Use linear mapping according to Zarringhalam et al</option>
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93 <option value="C">C: Use a cutoff−approach to divide into paired and unpaired nucleotides</option>
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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>
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95 <option value="L">L: Use a linear model to convert the reactivity into a probability for being unpaired</option>
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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>
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97 </param>
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98 <when value="M">
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99 </when>
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100 <when value="C">
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101 <param name="c" type="float" value="0.25" label="Cutoff"/>
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102 </when>
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103 <when value="S">
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104 </when>
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105 <when value="L">
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106 <param name="s" type="float" value="0.68" label="Slope"/>
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107 <param name="i" type="float" value="0.2" label="Intercept"/>
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108 </when>
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109 <when value="O">
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110 <param name="s" type="float" value="1.6" label="Slope s"/>
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111 <param name="i" type="float" value="-2.29" label="Intercept"/>
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112 </when>
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113 </conditional>
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114 </when>
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115 <when value="W">
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116 </when>
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117 </conditional>
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118 </when>
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119 <when value="notUsed">
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120 </when>
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121 </conditional>
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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 </inputs>
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127 <outputs>
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128 <data format="txt" name="tabularFile"/>
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129 </outputs>
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130 <tests>
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131 <test>
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132 <param name="input" value="rnaeval_input1.dbn"/>
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133 <output name="out_file" file="rnaeval_result1.txt"/>
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134 </test>
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135 </tests>
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136 <help>
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137 <![CDATA[
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138 **RNAeval**
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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.
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140
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141 -----
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142
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143 **Input format**
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144
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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.
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146
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147
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148 ------
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149
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150 **Outputs**
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151
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152 First line: the sequence, second line: the structure with its corresponding energy
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153
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154
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155 ]]>
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156 </help>
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157 <expand macro="citations" />
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158 </tool>