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0
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Profile length of microsatellites or short tandem repeats from short read data",
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4 "format-version": "0.1",
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5 "name": "microsatellite_profiling",
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6 "steps": {
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7 "0": {
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8 "annotation": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites",
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9 "id": 0,
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10 "input_connections": {},
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11 "inputs": [
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12 {
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13 "description": "input raw read that you want to detect Tandem reepats (TRs)/microsatellites",
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14 "name": "single end fastq"
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15 }
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16 ],
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17 "name": "Input dataset",
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18 "outputs": [],
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19 "position": {
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20 "left": 200,
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21 "top": 274.765625
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22 },
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23 "tool_errors": null,
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24 "tool_id": null,
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25 "tool_state": "{\"name\": \"single end fastq\"}",
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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": "need to be prepared by user using TR genome profiling",
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32 "id": 1,
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33 "input_connections": {},
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34 "inputs": [
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35 {
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36 "description": "need to be prepared by user using TR genome profiling",
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37 "name": "TR in genome"
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38 }
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39 ],
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40 "name": "Input dataset",
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41 "outputs": [],
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42 "position": {
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43 "left": 177,
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44 "top": 412.953125
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45 },
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46 "tool_errors": null,
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47 "tool_id": null,
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48 "tool_state": "{\"name\": \"TR in genome\"}",
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49 "tool_version": null,
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50 "type": "data_input",
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51 "user_outputs": []
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52 },
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53 "2": {
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54 "annotation": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files",
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55 "id": 2,
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56 "input_connections": {},
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57 "inputs": [
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58 {
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59 "description": "https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files",
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60 "name": "error rate file"
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61 }
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62 ],
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63 "name": "Input dataset",
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64 "outputs": [],
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65 "position": {
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66 "left": 1412.875,
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67 "top": 384.671875
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68 },
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69 "tool_errors": null,
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70 "tool_id": null,
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71 "tool_state": "{\"name\": \"error rate file\"}",
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72 "tool_version": null,
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73 "type": "data_input",
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74 "user_outputs": []
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75 },
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76 "3": {
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77 "annotation": "",
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78 "id": 3,
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79 "input_connections": {
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80 "filePath": {
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81 "id": 0,
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82 "output_name": "output"
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83 }
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84 },
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85 "inputs": [],
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86 "name": "Microsatellite detection",
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87 "outputs": [
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88 {
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89 "name": "stdout",
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90 "type": "tabular"
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91 }
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92 ],
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93 "position": {
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94 "left": 441.953125,
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95 "top": 252
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96 },
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97 "post_job_actions": {
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98 "ChangeDatatypeActionstdout": {
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99 "action_arguments": {
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100 "newtype": "tabular"
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101 },
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102 "action_type": "ChangeDatatypeAction",
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103 "output_name": "stdout"
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104 },
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105 "RenameDatasetActionstdout": {
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106 "action_arguments": {
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107 "newname": "TR in raw reads"
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108 },
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109 "action_type": "RenameDatasetAction",
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110 "output_name": "stdout"
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111 }
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112 },
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113 "tool_errors": null,
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114 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/microsatellite/1.0.0",
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115 "tool_state": "{\"__page__\": 0, \"flankSetting\": \"{\\\"noflankdisplay\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"filePath\": \"null\", \"minlength\": \"\\\"5\\\"\", \"hammingThreshold\": \"\\\"0\\\"\", \"period\": \"\\\"1\\\"\", \"surfix\": \"\\\"20\\\"\", \"prefix\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"inputFileSource\": \"{\\\"inputFileType\\\": \\\"fastq\\\", \\\"__current_case__\\\": 3}\", \"partialmotifs\": \"\\\"True\\\"\", \"multipleruns\": \"\\\"True\\\"\"}",
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116 "tool_version": "1.0.0",
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117 "type": "tool",
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118 "user_outputs": []
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119 },
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120 "4": {
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121 "annotation": "",
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122 "id": 4,
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123 "input_connections": {
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124 "input": {
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125 "id": 3,
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126 "output_name": "stdout"
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127 }
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128 },
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129 "inputs": [],
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130 "name": "Read name modifier",
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131 "outputs": [
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132 {
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133 "name": "output",
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134 "type": "tabular"
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135 }
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136 ],
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137 "position": {
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138 "left": 418.484375,
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139 "top": 385.03125
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140 },
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141 "post_job_actions": {},
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142 "tool_errors": null,
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143 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/space2underscore_readname/1.0.0",
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144 "tool_state": "{\"__page__\": 0, \"column_n\": \"\\\"6\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\"}",
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145 "tool_version": "1.0.0",
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146 "type": "tool",
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147 "user_outputs": []
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148 },
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149 "5": {
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150 "annotation": "",
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151 "id": 5,
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152 "input_connections": {
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153 "microsat_in_read": {
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154 "id": 4,
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155 "output_name": "output"
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156 }
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157 },
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158 "inputs": [],
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159 "name": "Fetch flanking bases",
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160 "outputs": [
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161 {
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162 "name": "Leftflanking",
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163 "type": "fastq"
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164 },
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165 {
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166 "name": "Rightflanking",
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167 "type": "fastq"
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168 }
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169 ],
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170 "position": {
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171 "left": 390.9375,
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172 "top": 509.046875
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173 },
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174 "post_job_actions": {
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175 "ChangeDatatypeActionLeftflanking": {
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176 "action_arguments": {
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177 "newtype": "fastqsanger"
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178 },
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179 "action_type": "ChangeDatatypeAction",
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180 "output_name": "Leftflanking"
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181 },
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182 "ChangeDatatypeActionRightflanking": {
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183 "action_arguments": {
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184 "newtype": "fastqsanger"
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185 },
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186 "action_type": "ChangeDatatypeAction",
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187 "output_name": "Rightflanking"
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188 },
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189 "HideDatasetActionLeftflanking": {
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190 "action_arguments": {},
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191 "action_type": "HideDatasetAction",
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192 "output_name": "Leftflanking"
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193 },
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194 "HideDatasetActionRightflanking": {
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195 "action_arguments": {},
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196 "action_type": "HideDatasetAction",
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197 "output_name": "Rightflanking"
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198 }
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199 },
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200 "tool_errors": null,
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201 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/fetchflank/1.0.0",
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202 "tool_state": "{\"qualitycutoff\": \"\\\"20\\\"\", \"lengthofbasetocheckquality\": \"\\\"20\\\"\", \"__rerun_remap_job_id__\": null, \"microsat_in_read\": \"null\", \"__page__\": 0}",
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203 "tool_version": "1.0.0",
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204 "type": "tool",
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205 "user_outputs": []
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206 },
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207 "6": {
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208 "annotation": "this tool has problems with parameter setting when you run it from pipeline. If you want different parameter, it's recommend that you clone pipleline and modify it.",
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209 "id": 6,
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210 "input_connections": {
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211 "paired|input1": {
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212 "id": 5,
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213 "output_name": "Leftflanking"
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214 },
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215 "paired|input2": {
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216 "id": 5,
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217 "output_name": "Rightflanking"
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218 }
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219 },
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220 "inputs": [],
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221 "name": "Map with BWA for Illumina",
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222 "outputs": [
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223 {
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224 "name": "output",
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225 "type": "sam"
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226 }
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227 ],
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228 "position": {
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229 "left": 403,
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230 "top": 686
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231 },
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232 "post_job_actions": {
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233 "HideDatasetActionoutput": {
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234 "action_arguments": {},
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235 "action_type": "HideDatasetAction",
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236 "output_name": "output"
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237 }
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238 },
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239 "tool_errors": null,
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240 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3",
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241 "tool_state": "{\"genomeSource\": \"{\\\"refGenomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 1}\", \"params\": \"{\\\"outputTopN\\\": \\\"3\\\", \\\"suboptAlign\\\": \\\"\\\", \\\"gapOpenPenalty\\\": \\\"11\\\", \\\"maxGapOpens\\\": \\\"1\\\", \\\"mismatchPenalty\\\": \\\"3\\\", \\\"fracMissingAligns\\\": \\\"0.04\\\", \\\"disallowIndel\\\": \\\"5\\\", \\\"outputTopNDisc\\\": \\\"10\\\", \\\"disallowLongDel\\\": \\\"16\\\", \\\"readGroup\\\": {\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}, \\\"maxInsertSize\\\": \\\"500\\\", \\\"__current_case__\\\": 1, \\\"maxEditDist\\\": \\\"0\\\", \\\"gapExtensPenalty\\\": \\\"4\\\", \\\"maxGapExtens\\\": \\\"-1\\\", \\\"maxEditDistSeed\\\": \\\"2\\\", \\\"noIterSearch\\\": \\\"False\\\", \\\"seed\\\": \\\"-1\\\", \\\"maxOccurPairing\\\": \\\"100000\\\", \\\"source_select\\\": \\\"full\\\"}\", \"suppressHeader\": \"\\\"False\\\"\"}",
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242 "tool_version": "1.2.3",
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243 "type": "tool",
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244 "user_outputs": []
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245 },
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246 "7": {
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247 "annotation": "",
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248 "id": 7,
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249 "input_connections": {
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250 "input1": {
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251 "id": 6,
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252 "output_name": "output"
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253 }
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254 },
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255 "inputs": [],
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256 "name": "Filter SAM",
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257 "outputs": [
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258 {
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259 "name": "out_file1",
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260 "type": "sam"
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261 }
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262 ],
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263 "position": {
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264 "left": 778,
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265 "top": 489.953125
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266 },
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267 "post_job_actions": {
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268 "HideDatasetActionout_file1": {
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269 "action_arguments": {},
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270 "action_type": "HideDatasetAction",
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271 "output_name": "out_file1"
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272 }
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273 },
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274 "tool_errors": null,
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275 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0",
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276 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"bits\": \"[{\\\"states\\\": \\\"0\\\", \\\"__index__\\\": 0, \\\"flags\\\": \\\"--0x0004\\\"}]\"}",
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277 "tool_version": "1.0.0",
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278 "type": "tool",
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279 "user_outputs": []
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280 },
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281 "8": {
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282 "annotation": "remove all mapped read with soft mask",
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283 "id": 8,
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284 "input_connections": {
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285 "input": {
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286 "id": 7,
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287 "output_name": "out_file1"
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288 }
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289 },
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290 "inputs": [],
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291 "name": "Filter",
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292 "outputs": [
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293 {
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294 "name": "out_file1",
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295 "type": "input"
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296 }
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297 ],
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298 "position": {
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299 "left": 781.5,
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300 "top": 602
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301 },
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302 "post_job_actions": {
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303 "HideDatasetActionout_file1": {
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304 "action_arguments": {},
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305 "action_type": "HideDatasetAction",
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306 "output_name": "out_file1"
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307 }
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308 },
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309 "tool_errors": null,
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310 "tool_id": "Filter1",
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311 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"header_lines\": \"\\\"0\\\"\", \"cond\": \"\\\"c6.count('S')==0\\\"\", \"__page__\": 0}",
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312 "tool_version": "1.1.0",
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313 "type": "tool",
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314 "user_outputs": []
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315 },
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316 "9": {
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317 "annotation": "",
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318 "id": 9,
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319 "input_connections": {
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320 "input": {
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321 "id": 8,
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322 "output_name": "out_file1"
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323 }
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324 },
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325 "inputs": [],
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326 "name": "Sort",
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327 "outputs": [
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328 {
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329 "name": "out_file1",
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330 "type": "input"
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331 }
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332 ],
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333 "position": {
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334 "left": 777.5,
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335 "top": 739
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336 },
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337 "post_job_actions": {
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338 "HideDatasetActionout_file1": {
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339 "action_arguments": {},
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340 "action_type": "HideDatasetAction",
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341 "output_name": "out_file1"
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342 }
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343 },
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344 "tool_errors": null,
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345 "tool_id": "sort1",
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346 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[]\"}",
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347 "tool_version": "1.0.3",
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348 "type": "tool",
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349 "user_outputs": []
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350 },
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351 "10": {
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352 "annotation": "",
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353 "id": 10,
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354 "input_connections": {
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355 "flankedbasesSAM": {
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356 "id": 9,
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357 "output_name": "out_file1"
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358 }
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359 },
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360 "inputs": [],
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361 "name": "Combine mapped flaked bases",
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362 "outputs": [
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363 {
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364 "name": "output",
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365 "type": "tabular"
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366 }
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367 ],
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368 "position": {
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369 "left": 723.328125,
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370 "top": 887.828125
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371 },
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372 "post_job_actions": {
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373 "HideDatasetActionoutput": {
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374 "action_arguments": {},
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375 "action_type": "HideDatasetAction",
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376 "output_name": "output"
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377 }
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378 },
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379 "tool_errors": null,
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380 "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/PEsortedSAM2readprofile/1.0.0",
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381 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"maxoriginalreadlength\": \"\\\"101\\\"\", \"maxTRlength\": \"\\\"100\\\"\", \"flankedbasesSAM\": \"null\", \"twobitref\": \"null\"}",
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382 "tool_version": "1.0.0",
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383 "type": "tool",
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384 "user_outputs": []
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385 },
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386 "11": {
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387 "annotation": "",
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388 "id": 11,
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389 "input_connections": {
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390 "input1": {
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391 "id": 4,
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