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1 <tool id="antarna" name="antaRNA" version="1.1">
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2 <description>
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3 Ant Colony Optimized RNA Sequence Design
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4 </description>
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5 <requirements>
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3
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6 <requirement type="package" version="2.2.12">pkiss</requirement>
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7 <requirement type="package" version="3.2.5">rnashapes</requirement>
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8 <requirement type="package" version="1.8">numpy</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code level="fatal" range="1:"/>
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12 </stdio>
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13 <version_command>python antaRNA.py --version</version_command>
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14 <command interpreter="python"><![CDATA[antaRNA.py
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15 #if $Cstr and $Cstr is not None:
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16 -Cstr "$Cstr"
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17 #end if
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18
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19 #if $tGC and $tGC is not None:
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20 -tGC $tGC
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21 #end if
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22
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23 #if $n and $n is not None:
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24 -n $n
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25 #end if
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26 $GU
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27
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28 #if $s and $s is not None:
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29 -s $s
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30 #end if
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31
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32 #if $ip and $ip is not None:
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33 -ip $ip
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34 #end if
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35
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36 #if $r and $r is not None:
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37 -r $r
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38 #end if
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39
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40 #if $CC and $CC is not None:
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41 -CC $CC
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42 #end if
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43
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44 #if $aTC and $aTC is not None:
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45 -aTC $aTC
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46 #end if
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47 $p
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48 $pkPar
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49
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50 #if $strategy and $strategy is not None:
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51 --strategy $strategy
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52 #end if
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53
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54 #if $tGCmax and $tGCmax is not None:
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55 -tGCmax $tGCmax
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56 #end if
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57
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58 #if $tGCvar and $tGCvar is not None:
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59 -tGCvar $tGCvar
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60 #end if
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61
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62 #if $t and $t is not None:
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63 -t $t
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64 #end if
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65
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66 #if $P and $P is not None:
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67 -P $P
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68 #end if
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69
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70 #if $of and $of is not None:
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71 -of $of
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72 #end if
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73
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74 #if $Cseq and $Cseq is not None:
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75 -Cseq $Cseq
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76 #end if
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77
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78 #if $l and $l is not None:
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79 -l $l
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80 #end if
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81
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82 #if $name and $name is not None:
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83 --name $name
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84 #end if
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85
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86 #if $a and $a is not None:
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87 -a $a
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88 #end if
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89
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90 #if $b and $b is not None:
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91 -b $b
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92 #end if
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93
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94 #if $er and $er is not None:
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95 -er $er
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96 #end if
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97
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98 #if $Cstrw and $Cstrw is not None:
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99 -Cstrw $Cstrw
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100 #end if
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101
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102 #if $Cgcw and $Cgcw is not None:
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103 -Cgcw $Cgcw
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104 #end if
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105
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106 #if $Cseqw and $Cseqw is not None:
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107 -Cseqw $Cseqw
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108 #end if
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109 $v
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110 $ov
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111 > $default]]></command>
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112 <inputs>
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113 <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint. (-Cstr)" name="Cstr" type="text"/>
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114 <param label="Objective target GC content in [0,1]. (-tGC)" name="tGC" type="float" value="0"/>
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115 <param label="Number of sequences which shall be produced. (-n)" name="n" type="integer" value="0"/>
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116 <param checked="false" label="Allowing GU base pairs. (-GU)" name="GU" type="boolean" truevalue="-GU" falsevalue=""/>
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117 <param default="none" label="Provides a seed value for the used pseudo random number generator. (-s)" name="s" type="text"/>
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118 <param default="s" label="Select the improving method. h=hierarchical, s=score_based. (-ip)" name="ip" type="text"/>
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119 <param label="Amount of maximal terrain resets, until the best solution is retuned as solution. (-r)" name="r" type="integer" value="5"/>
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120 <param label="Delimits the convergence count criterion for a reset. (-CC)" name="CC" type="integer" value="130"/>
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121 <param label="Delimits the amount of internal ants for termination convergence criterion for a reset. (-aTC)" name="aTC" type="integer" value="50"/>
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122 <param checked="false" label="Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!! (-p)" name="p" type="boolean" truevalue="-p" falsevalue=""/>
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123 <param checked="false" label="Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored). (-pkPar)" name="pkPar" type="boolean" truevalue="-pkPar" falsevalue=""/>
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124 <param default="A" label="Defining the pKiss folding strategy. (--strategy)" name="strategy" type="text"/>
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125 <param label="Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value. (-tGCmax)" name="tGCmax" type="float" value="-1.0"/>
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126 <param label="Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu). (-tGCvar)" name="tGCvar" type="float" value="-1.0"/>
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127 <param label="Provides a temperature for the folding algorithms. (-t)" name="t" type="float" value="37.0"/>
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128 <param default="" label="Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold. (-P)" name="P" type="text"/>
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129 <param default="STDOUT" label="Provide a path and an output file, e.g. "/path/to/the/target_file". (-of)" name="of" type="text"/>
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130 <param default="" label="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card "N". (-Cseq)" name="Cseq" type="text"/>
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131 <param label="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence]. (-l)" name="l" type="integer" value="1"/>
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132 <param default="antaRNA_" label="Defines a name which is used in the sequence output. (--name)" name="name" type="text"/>
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133 <param label="Sets alpha, probability weight for terrain path influence. [0,1] (-a)" name="a" type="float" value="1.0"/>
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134 <param label="Sets beta, probability weight for terrain pheromone influence. [0,1] (-b)" name="b" type="float" value="1.0"/>
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135 <param label="Pheromone evaporation rate. (-er)" name="er" type="float" value="0.2"/>
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136 <param label="Structure constraint quality weighting factor. [0,1] (-Cstrw)" name="Cstrw" type="float" value="0.5"/>
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137 <param label="GC content constraint quality weighting factor. [0,1] (-Cgcw)" name="Cgcw" type="float" value="5.0"/>
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138 <param label="Sequence constraint quality weighting factor. [0,1] (-Cseqw)" name="Cseqw" type="float" value="1.0"/>
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139 <param checked="false" label="Displayes intermediate output. (-v)" name="v" type="boolean" truevalue="-v" falsevalue=""/>
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140 <param checked="false" label="Prints additional output to the headers of the produced sequences. (-ov)" name="ov" type="boolean" truevalue="-ov" falsevalue=""/>
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141 </inputs>
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142 <outputs>
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143 <data format="txt" hidden="false" name="default"/>
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144 </outputs>
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145 <help><![CDATA[
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146 .
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147
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148 ===========================
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149 antaRNA - ant assembled RNA
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150 ===========================
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151
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152 - antaRNA uses the VIENNNA RNA Package
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153 - specifically it uses RNAfold and RNAdistance to calculate energies of and distances between secondary structures (version 2.1.x)
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154 - for the parametrization of antaRNA the version 2.1.3 of the ViennaRNA package was used
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155
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156
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157 - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
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158
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159 Example calls:
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160
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161 - python antaRNA.py --Cstr "...(((...)))..." --tGC 0.5 -n 2
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162 - python antaRNA.py --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
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163 - python antaRNA.py --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
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164 ]]></help>
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165 </tool>
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166
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