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1 <tool id="EMBOSS: syco96" name="syco" version="5.0.0">
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2 <!-- graphics output -->
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3 <description>Synonymous codon usage Gribskov statistic plot</description>
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4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
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6 -auto</command>
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7 <inputs>
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8 <param format="fasta" name="input1" type="data">
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9 <label>Sequence</label>
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10 </param>
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11 <param name="cfile" type="select">
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12 <label>Codon Usage File</label>
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13 <option value="Ehum.cut">Ehum.cut</option>
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14 <option value="Eyeastcai.cut">Eyeastcai.cut</option>
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15 <option value="Eacc.cut">Eacc.cut</option>
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16 <option value="Eadenovirus5.cut">Eadenovirus5.cut</option>
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17 <option value="Eadenovirus7.cut">Eadenovirus7.cut</option>
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18 <option value="Eaidlav.cut">Eaidlav.cut</option>
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19 <option value="Eanasp.cut">Eanasp.cut</option>
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20 <option value="Eani.cut">Eani.cut</option>
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21 <option value="Eani_h.cut">Eani_h.cut</option>
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22 <option value="Eanidmit.cut">Eanidmit.cut</option>
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23 <option value="Easn.cut">Easn.cut</option>
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24 <option value="Eath.cut">Eath.cut</option>
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25 <option value="Eatu.cut">Eatu.cut</option>
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26 <option value="Eavi.cut">Eavi.cut</option>
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27 <option value="Ebja.cut">Ebja.cut</option>
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28 <option value="Ebly.cut">Ebly.cut</option>
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29 <option value="Ebme.cut">Ebme.cut</option>
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30 <option value="Ebmo.cut">Ebmo.cut</option>
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31 <option value="Ebna.cut">Ebna.cut</option>
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32 <option value="Ebov.cut">Ebov.cut</option>
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33 <option value="Ebovsp.cut">Ebovsp.cut</option>
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34 <option value="Ebst.cut">Ebst.cut</option>
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35 <option value="Ebsu.cut">Ebsu.cut</option>
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36 <option value="Ebsu_h.cut">Ebsu_h.cut</option>
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37 <option value="Ecac.cut">Ecac.cut</option>
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38 <option value="Ecal.cut">Ecal.cut</option>
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39 <option value="Eccr.cut">Eccr.cut</option>
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40 <option value="Ecel.cut">Ecel.cut</option>
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41 <option value="Echi.cut">Echi.cut</option>
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42 <option value="Echicken.cut">Echicken.cut</option>
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43 <option value="Echisp.cut">Echisp.cut</option>
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44 <option value="Echk.cut">Echk.cut</option>
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45 <option value="Echmp.cut">Echmp.cut</option>
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46 <option value="Echnt.cut">Echnt.cut</option>
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47 <option value="Echos.cut">Echos.cut</option>
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48 <option value="Echzm.cut">Echzm.cut</option>
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49 <option value="Echzmrubp.cut">Echzmrubp.cut</option>
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50 <option value="Ecpx.cut">Ecpx.cut</option>
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51 <option value="Ecre.cut">Ecre.cut</option>
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52 <option value="Ecrisp.cut">Ecrisp.cut</option>
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53 <option value="Ectr.cut">Ectr.cut</option>
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54 <option value="Edayhoff.cut">Edayhoff.cut</option>
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55 <option value="Eddi.cut">Eddi.cut</option>
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56 <option value="Eddi_h.cut">Eddi_h.cut</option>
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57 <option value="Edog.cut">Edog.cut</option>
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58 <option value="Edro.cut">Edro.cut</option>
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59 <option value="Edro_h.cut">Edro_h.cut</option>
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60 <option value="Edrosophila.cut">Edrosophila.cut</option>
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61 <option value="Eeca.cut">Eeca.cut</option>
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62 <option value="Eeco.cut">Eeco.cut</option>
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63 <option value="Eeco_h.cut">Eeco_h.cut</option>
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64 <option value="Eecoli.cut">Eecoli.cut</option>
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65 <option value="Ef1.cut">Ef1.cut</option>
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66 <option value="Efish.cut">Efish.cut</option>
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67 <option value="Efmdvpolyp.cut">Efmdvpolyp.cut</option>
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68 <option value="Eham.cut">Eham.cut</option>
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69 <option value="Ehha.cut">Ehha.cut</option>
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70 <option value="Ehin.cut">Ehin.cut</option>
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71 <option value="Ehma.cut">Ehma.cut</option>
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72 <option value="Ehuman.cut">Ehuman.cut</option>
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73 <option value="Ekla.cut">Ekla.cut</option>
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74 <option value="Ekpn.cut">Ekpn.cut</option>
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75 <option value="Ella.cut">Ella.cut</option>
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76 <option value="Emac.cut">Emac.cut</option>
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77 <option value="Emaize.cut">Emaize.cut</option>
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78 <option value="Emam_h.cut">Emam_h.cut</option>
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79 <option value="Emixlg.cut">Emixlg.cut</option>
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80 <option value="Emouse.cut">Emouse.cut</option>
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81 <option value="Emsa.cut">Emsa.cut</option>
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82 <option value="Emse.cut">Emse.cut</option>
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83 <option value="Emta.cut">Emta.cut</option>
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84 <option value="Emtu.cut">Emtu.cut</option>
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85 <option value="Emus.cut">Emus.cut</option>
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86 <option value="Emussp.cut">Emussp.cut</option>
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87 <option value="Emva.cut">Emva.cut</option>
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88 <option value="Emze.cut">Emze.cut</option>
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89 <option value="Emzecp.cut">Emzecp.cut</option>
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90 <option value="Encr.cut">Encr.cut</option>
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91 <option value="Eneu.cut">Eneu.cut</option>
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92 <option value="Engo.cut">Engo.cut</option>
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93 <option value="Eoncsp.cut">Eoncsp.cut</option>
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94 <option value="Epae.cut">Epae.cut</option>
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95 <option value="Epea.cut">Epea.cut</option>
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96 <option value="Epet.cut">Epet.cut</option>
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97 <option value="Epfa.cut">Epfa.cut</option>
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98 <option value="Ephix174.cut">Ephix174.cut</option>
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99 <option value="Ephv.cut">Ephv.cut</option>
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100 <option value="Ephy.cut">Ephy.cut</option>
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101 <option value="Epig.cut">Epig.cut</option>
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102 <option value="Epolyomaa2.cut">Epolyomaa2.cut</option>
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103 <option value="Epombe.cut">Epombe.cut</option>
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104 <option value="Epombecai.cut">Epombecai.cut</option>
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105 <option value="Epot.cut">Epot.cut</option>
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106 <option value="Eppu.cut">Eppu.cut</option>
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107 <option value="Epse.cut">Epse.cut</option>
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108 <option value="Epsy.cut">Epsy.cut</option>
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109 <option value="Epvu.cut">Epvu.cut</option>
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110 <option value="Erab.cut">Erab.cut</option>
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111 <option value="Erabbit.cut">Erabbit.cut</option>
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112 <option value="Erabsp.cut">Erabsp.cut</option>
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113 <option value="Erat.cut">Erat.cut</option>
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114 <option value="Eratsp.cut">Eratsp.cut</option>
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115 <option value="Erca.cut">Erca.cut</option>
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116 <option value="Erhm.cut">Erhm.cut</option>
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117 <option value="Eric.cut">Eric.cut</option>
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118 <option value="Erle.cut">Erle.cut</option>
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119 <option value="Erme.cut">Erme.cut</option>
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120 <option value="Ersp.cut">Ersp.cut</option>
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121 <option value="Esalsp.cut">Esalsp.cut</option>
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122 <option value="Esau.cut">Esau.cut</option>
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123 <option value="Esco.cut">Esco.cut</option>
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124 <option value="Esgi.cut">Esgi.cut</option>
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125 <option value="Eshp.cut">Eshp.cut</option>
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126 <option value="Eshpsp.cut">Eshpsp.cut</option>
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127 <option value="Esli.cut">Esli.cut</option>
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128 <option value="Eslm.cut">Eslm.cut</option>
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129 <option value="Esma.cut">Esma.cut</option>
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130 <option value="Esmi.cut">Esmi.cut</option>
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131 <option value="Esmu.cut">Esmu.cut</option>
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132 <option value="Esoy.cut">Esoy.cut</option>
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133 <option value="Espi.cut">Espi.cut</option>
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134 <option value="Espn.cut">Espn.cut</option>
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135 <option value="Espo.cut">Espo.cut</option>
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136 <option value="Espo_h.cut">Espo_h.cut</option>
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137 <option value="Espu.cut">Espu.cut</option>
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138 <option value="Esta.cut">Esta.cut</option>
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139 <option value="Esty.cut">Esty.cut</option>
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140 <option value="Esus.cut">Esus.cut</option>
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141 <option value="Esv40.cut">Esv40.cut</option>
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142 <option value="Esyhsp.cut">Esyhsp.cut</option>
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143 <option value="Esynsp.cut">Esynsp.cut</option>
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144 <option value="Etbr.cut">Etbr.cut</option>
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145 <option value="Etcr.cut">Etcr.cut</option>
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146 <option value="Eter.cut">Eter.cut</option>
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147 <option value="Etetsp.cut">Etetsp.cut</option>
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148 <option value="Etob.cut">Etob.cut</option>
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149 <option value="Etobcp.cut">Etobcp.cut</option>
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150 <option value="Etom.cut">Etom.cut</option>
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151 <option value="Etrb.cut">Etrb.cut</option>
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152 <option value="Evco.cut">Evco.cut</option>
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153 <option value="Ewht.cut">Ewht.cut</option>
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154 <option value="Exel.cut">Exel.cut</option>
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155 <option value="Exenopus.cut">Exenopus.cut</option>
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156 <option value="Eyeast.cut">Eyeast.cut</option>
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157 <option value="Eyen.cut">Eyen.cut</option>
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158 <option value="Eysc.cut">Eysc.cut</option>
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159 <option value="Eysc_h.cut">Eysc_h.cut</option>
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160 <option value="Eyscmt.cut">Eyscmt.cut</option>
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161 <option value="Eysp.cut">Eysp.cut</option>
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162 <option value="Ezebrafish.cut">Ezebrafish.cut</option>
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163 <option value="Ezma.cut">Ezma.cut</option>
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164 </param>
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165 <param name="window" size="4" type="text" value="30">
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166 <label>Averaging window</label>
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167 </param>
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168 <param name="uncommon" type="select">
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169 <label>Show common codon usage</label>
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170 <option value="no">No</option>
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171 <option value="yes">Yes</option>
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172 </param>
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173 <param name="minimum" size="4" type="text" value="0.15">
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174 <label>Minimum value for a common codon</label>
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175 </param>
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176 </inputs>
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177 <outputs>
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178 <data format="png" name="ofile1" />
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179 <data format="syco" name="ofile2" />
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180 </outputs>
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181 <!-- <tests>
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182 <test>
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183 <param name="input1" value="2.fasta"/>
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184 <param name="cfile" value="Ehum.cut"/>
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185 <param name="window" value="30"/>
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186 <param name="uncommon" value="no"/>
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187 <param name="minimum" value="0.15"/>
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188 <output name="ofile2" file="emboss_syco_out.syco"/>
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189 </test>
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190 </tests> -->
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191 <help>
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192
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193 You can view the original documentation here_.
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194
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195 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html
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196 </help>
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197 </tool>
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