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1 {
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3 "annotation": "glimmer-from-scratch",
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4 "format-version": "0.1",
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5 "name": "Glimmer",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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10 "input_connections": {},
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11 "inputs": [
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12 {
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14 "name": "Genome sequence"
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15 }
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16 ],
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18 "outputs": [],
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22 },
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26 "tool_version": null,
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27 "type": "data_input",
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28 "user_outputs": []
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29 },
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30 "1": {
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31 "annotation": "",
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33 "input_connections": {
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34 "loSequence": {
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35 "id": 0,
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36 "output_name": "output"
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37 }
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38 },
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39 "inputs": [],
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40 "name": "Long-ORFs",
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41 "outputs": [
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42 {
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44 "type": "txt"
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45 },
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46 {
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47 "name": "loOutput",
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48 "type": "glimmer_coords"
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49 }
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50 ],
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51 "position": {
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54 },
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59 "tool_version": "0.2",
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60 "type": "tool",
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61 "user_outputs": []
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62 },
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63 "2": {
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66 "input_connections": {
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70 },
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74 }
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75 },
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76 "inputs": [],
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77 "name": "Extract",
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78 "outputs": [
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79 {
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80 "name": "logfile",
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81 "type": "txt"
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82 },
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83 {
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84 "name": "exOutput",
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85 "type": "fasta"
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86 }
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87 ],
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88 "position": {
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89 "left": 659,
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90 "top": 231
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91 },
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92 "post_job_actions": {},
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93 "tool_errors": null,
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94 "tool_id": "extract_wrapper",
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95 "tool_state": "{\"__page__\": 0, \"exSequence\": \"null\", \"exCoords\": \"null\", \"exDir\": \"\\\"False\\\"\", \"exNoStop\": \"\\\"False\\\"\", \"exNoStart\": \"\\\"False\\\"\", \"exNoWrap\": \"\\\"False\\\"\", \"exMinLen\": \"\\\"\\\"\", \"ex2Fields\": \"\\\"False\\\"\"}",
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96 "tool_version": "0.2",
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97 "type": "tool",
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98 "user_outputs": []
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99 },
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101 "annotation": "",
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102 "id": 3,
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103 "input_connections": {
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104 "biSequence": {
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106 "output_name": "exOutput"
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107 }
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108 },
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109 "inputs": [],
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110 "name": "Build-ICM",
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111 "outputs": [
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112 {
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113 "name": "logfile",
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114 "type": "txt"
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115 },
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116 {
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117 "name": "biIcm",
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118 "type": "glimmer_icm"
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119 }
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120 ],
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121 "position": {
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123 "top": 715
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124 },
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125 "post_job_actions": {},
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126 "tool_errors": null,
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127 "tool_id": "build-icm_wrapper",
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128 "tool_state": "{\"__page__\": 0, \"biStopCodons\": \"\\\"\\\"\", \"biPeriod\": \"\\\"3\\\"\", \"biTransTable\": \"\\\"\\\"\", \"biNoStops\": \"\\\"False\\\"\", \"biDepth\": \"\\\"7\\\"\", \"biReverse\": \"\\\"False\\\"\", \"biSequence\": \"null\", \"biWidth\": \"\\\"12\\\"\"}",
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129 "tool_version": "0.2",
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130 "type": "tool",
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131 "user_outputs": []
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132 },
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133 "4": {
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134 "annotation": "",
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135 "id": 4,
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136 "input_connections": {
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137 "glIcm": {
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138 "id": 3,
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139 "output_name": "biIcm"
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140 },
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141 "glSequence": {
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142 "id": 0,
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143 "output_name": "output"
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144 }
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145 },
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146 "inputs": [],
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147 "name": "Glimmer3",
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148 "outputs": [
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149 {
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150 "name": "logfile",
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151 "type": "txt"
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152 },
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153 {
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154 "name": "glDetail",
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155 "type": "txt"
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156 },
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157 {
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158 "name": "glPredict",
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159 "type": "txt"
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160 }
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161 ],
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162 "position": {
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163 "left": 508,
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164 "top": 715
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165 },
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166 "post_job_actions": {},
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167 "tool_errors": null,
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168 "tool_id": "glimmer3_wrapper",
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169 "tool_state": "{\"__page__\": 0, \"glFirstCodon\": \"\\\"False\\\"\", \"glNoIndep\": \"\\\"False\\\"\", \"glIcm\": \"null\", \"glRbsPwm\": \"null\", \"glEntropy\": \"null\", \"glSeparateGenes\": \"\\\"False\\\"\", \"glOrfCoords\": \"null\", \"glMaxOverlap\": \"\\\"\\\"\", \"glIgnoreScoreLen\": \"\\\"\\\"\", \"glGcPercent\": \"\\\"\\\"\", \"glSequence\": \"null\", \"glGeneLen\": \"\\\"\\\"\", \"glStopCodons\": \"\\\"\\\"\", \"glExtend\": \"\\\"False\\\"\", \"glLinear\": \"\\\"False\\\"\", \"glTransTable\": \"\\\"\\\"\", \"glThreshold\": \"\\\"\\\"\", \"glStartCodons\": \"\\\"\\\"\", \"glStartProbs\": \"\\\"\\\"\"}",
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170 "tool_version": "0.2",
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171 "type": "tool",
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172 "user_outputs": []
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173 }
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174 }
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175 }
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