Mercurial > repos > john-mccallum > pcr_markers
annotate Galaxy-Workflow-CAPS_Marker_Development_from_454_Read_Mapping.ga @ 2:ea2117a7b363 draft
Uploaded CAPS marker design workflow for 454 Data
author | john-mccallum |
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date | Sun, 09 Sep 2012 23:16:56 -0400 |
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Uploaded CAPS marker design workflow for 454 Data
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1 { |
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2 "a_galaxy_workflow": "true", |
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3 "annotation": "", |
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4 "format-version": "0.1", |
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5 "name": "CAPS Marker Development from 454 Read Mapping", |
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6 "steps": { |
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7 "0": { |
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8 "annotation": "", |
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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": "", |
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14 "name": "Reference sequences" |
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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": 122.80303955078125, |
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21 "top": 119.77274131774902 |
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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\": \"Reference sequences\"}", |
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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": "Reads to map", |
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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": "Reads to map", |
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37 "name": "SFF File " |
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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": 104.6212158203125, |
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44 "top": 313.95454406738281 |
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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\": \"SFF File \"}", |
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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": "barcode, vector or adapter sequences to trim", |
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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": "barcode, vector or adapter sequences to trim", |
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60 "name": "Trimming 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": 195.727294921875, |
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67 "top": 544.8787841796875 |
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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\": \"Trimming 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 "ref_inputs_0|ref_input": { |
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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 "sff_inputs_0|sff_input": { |
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85 "id": 1, |
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86 "output_name": "output" |
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87 }, |
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88 "vt": { |
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89 "id": 2, |
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90 "output_name": "output" |
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91 } |
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92 }, |
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93 "inputs": [], |
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94 "name": "runMapping", |
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95 "outputs": [ |
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96 { |
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97 "name": "newbler_metrics", |
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98 "type": "txt" |
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99 }, |
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100 { |
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101 "name": "read_status", |
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102 "type": "tabular" |
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103 }, |
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104 { |
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105 "name": "trimmed_reads_fasta", |
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106 "type": "fasta" |
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107 }, |
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108 { |
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109 "name": "trimmed_reads_qual", |
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110 "type": "qual454" |
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111 }, |
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112 { |
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113 "name": "alignment_info", |
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114 "type": "tabular" |
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115 }, |
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116 { |
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117 "name": "all_contigs_fasta", |
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118 "type": "fasta" |
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119 }, |
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120 { |
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121 "name": "all_contigs_qual", |
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122 "type": "qual454" |
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123 }, |
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124 { |
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125 "name": "contigs_ace", |
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126 "type": "ace" |
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127 }, |
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128 { |
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129 "name": "large_contigs_fasta", |
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130 "type": "fasta" |
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131 }, |
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132 { |
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133 "name": "large_contigs_qual", |
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134 "type": "qual454" |
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135 }, |
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136 { |
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137 "name": "pair_align", |
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138 "type": "txt" |
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139 }, |
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140 { |
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141 "name": "pair_status", |
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142 "type": "tabular" |
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143 }, |
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144 { |
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145 "name": "scaffolds_fasta", |
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146 "type": "fasta" |
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147 }, |
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148 { |
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149 "name": "scaffolds_qual", |
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150 "type": "qual454" |
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151 }, |
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152 { |
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153 "name": "scaffolds_agp", |
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154 "type": "tabular" |
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155 }, |
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156 { |
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157 "name": "tag_pair_align", |
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158 "type": "txt" |
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159 }, |
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160 { |
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161 "name": "trim_status", |
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162 "type": "tabular" |
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163 }, |
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164 { |
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165 "name": "all_diffs", |
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166 "type": "tabular" |
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167 }, |
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168 { |
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169 "name": "all_struct_vars", |
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170 "type": "tabular" |
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171 }, |
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172 { |
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173 "name": "hc_diff", |
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174 "type": "tabular" |
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175 }, |
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176 { |
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177 "name": "hc_struct_vars", |
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178 "type": "tabular" |
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179 }, |
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180 { |
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181 "name": "gene_status", |
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182 "type": "tabular" |
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183 }, |
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184 { |
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185 "name": "mapping_qc", |
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186 "type": "xls" |
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187 }, |
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188 { |
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189 "name": "ref_status", |
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190 "type": "tabular" |
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191 } |
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192 ], |
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193 "position": { |
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194 "left": 432.71212768554688, |
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Uploaded CAPS marker design workflow for 454 Data
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195 "top": 330.90908813476562 |
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Uploaded CAPS marker design workflow for 454 Data
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196 }, |
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197 "post_job_actions": {}, |
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198 "tool_errors": null, |
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199 "tool_id": "toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.1", |
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200 "tool_state": "{\"minlen\": \"\\\"20\\\"\", \"rst\": \"\\\"12\\\"\", \"vs\": \"null\", \"vt\": \"null\", \"__page__\": 0, \"no\": \"\\\"\\\"\", \"paired_reads\": \"\\\"false\\\"\", \"notrim\": \"\\\"False\\\"\", \"tr\": \"\\\"-tr\\\"\", \"mcf\": \"null\", \"ref_type\": \"\\\"-gref\\\"\", \"newbler_exe\": \"\\\"runMapping\\\"\", \"info\": \"\\\"-info\\\"\", \"sanger_inputs\": \"[]\", \"sl\": \"\\\"16\\\"\", \"hsl\": \"\\\"70\\\"\", \"sanger_paired_inputs\": \"[]\", \"fe\": \"null\", \"pair\": \"\\\"\\\"\", \"fi\": \"null\", \"nor\": \"\\\"False\\\"\", \"a\": \"\\\"100\\\"\", \"sff_paired_inputs\": \"[]\", \"e\": \"\\\"0\\\"\", \"ace\": \"\\\"\\\"\", \"ss\": \"\\\"12\\\"\", \"ml\": \"\\\"40\\\"\", \"mi\": \"\\\"90\\\"\", \"l\": \"\\\"500\\\"\", \"ais\": \"\\\"2\\\"\", \"ref_inputs\": \"[{\\\"__index__\\\": 0, \\\"ref_input\\\": null}]\", \"srv\": \"\\\"False\\\"\", \"sff_inputs\": \"[{\\\"__index__\\\": 0, \\\"sff_input\\\": null}]\", \"sc\": \"\\\"1\\\"\", \"ud\": \"\\\"False\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"qo\": \"\\\"False\\\"\"}", |
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201 "tool_version": "1.0.1", |
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202 "type": "tool", |
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203 "user_outputs": [] |
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204 }, |
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205 "4": { |
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206 "annotation": "", |
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207 "id": 4, |
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208 "input_connections": { |
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209 "inputGsFile": { |
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210 "id": 3, |
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211 "output_name": "all_diffs" |
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212 } |
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Uploaded CAPS marker design workflow for 454 Data
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213 }, |
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214 "inputs": [], |
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215 "name": "Convert gsMapper to gff3", |
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216 "outputs": [ |
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217 { |
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218 "name": "outputfile", |
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219 "type": "gff3" |
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220 } |
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221 ], |
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222 "position": { |
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223 "left": 729.65148448944092, |
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Uploaded CAPS marker design workflow for 454 Data
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224 "top": 503.80300903320312 |
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Uploaded CAPS marker design workflow for 454 Data
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225 }, |
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226 "post_job_actions": {}, |
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227 "tool_errors": null, |
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228 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/gsMapper_to_gff3_1/1.0.0", |
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229 "tool_state": "{\"__page__\": 0, \"inputGsFile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\"}", |
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230 "tool_version": "1.0.0", |
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231 "type": "tool", |
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232 "user_outputs": [] |
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233 }, |
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234 "5": { |
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235 "annotation": "", |
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236 "id": 5, |
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237 "input_connections": { |
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238 "inputFasta": { |
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239 "id": 0, |
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240 "output_name": "output" |
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241 }, |
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242 "inputSNPGff3File": { |
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243 "id": 4, |
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244 "output_name": "outputfile" |
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245 } |
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246 }, |
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247 "inputs": [], |
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248 "name": "CAPS Detection", |
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249 "outputs": [ |
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250 { |
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251 "name": "outputfile", |
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252 "type": "interval" |
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253 } |
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254 ], |
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255 "position": { |
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256 "left": 994.77265930175781, |
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257 "top": 317.83332824707031 |
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258 }, |
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259 "post_job_actions": {}, |
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260 "tool_errors": null, |
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261 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0", |
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262 "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}", |
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263 "tool_version": "1.0.0", |
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264 "type": "tool", |
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265 "user_outputs": [] |
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266 }, |
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267 "6": { |
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268 "annotation": "", |
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269 "id": 6, |
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270 "input_connections": { |
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271 "input": { |
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272 "id": 5, |
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273 "output_name": "outputfile" |
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274 } |
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275 }, |
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276 "inputs": [], |
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277 "name": "Cut", |
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278 "outputs": [ |
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279 { |
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280 "name": "out_file1", |
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281 "type": "tabular" |
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282 } |
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283 ], |
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284 "position": { |
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285 "left": 1222.7424011230469, |
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286 "top": 314.98484802246094 |
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287 }, |
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288 "post_job_actions": {}, |
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289 "tool_errors": null, |
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290 "tool_id": "Cut1", |
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291 "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}", |
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292 "tool_version": "1.0.1", |
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293 "type": "tool", |
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294 "user_outputs": [] |
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295 }, |
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Uploaded CAPS marker design workflow for 454 Data
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296 "7": { |
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Uploaded CAPS marker design workflow for 454 Data
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297 "annotation": "", |
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Uploaded CAPS marker design workflow for 454 Data
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298 "id": 7, |
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Uploaded CAPS marker design workflow for 454 Data
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299 "input_connections": { |
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Uploaded CAPS marker design workflow for 454 Data
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300 "inputSNPfile": { |
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301 "id": 4, |
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302 "output_name": "outputfile" |
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Uploaded CAPS marker design workflow for 454 Data
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303 }, |
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Uploaded CAPS marker design workflow for 454 Data
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304 "inputTargetfile": { |
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Uploaded CAPS marker design workflow for 454 Data
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305 "id": 6, |
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306 "output_name": "out_file1" |
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Uploaded CAPS marker design workflow for 454 Data
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307 }, |
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Uploaded CAPS marker design workflow for 454 Data
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308 "inputfastaFile": { |
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Uploaded CAPS marker design workflow for 454 Data
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309 "id": 0, |
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Uploaded CAPS marker design workflow for 454 Data
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310 "output_name": "output" |
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311 } |
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Uploaded CAPS marker design workflow for 454 Data
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312 }, |
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Uploaded CAPS marker design workflow for 454 Data
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313 "inputs": [ |
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Uploaded CAPS marker design workflow for 454 Data
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314 { |
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Uploaded CAPS marker design workflow for 454 Data
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315 "description": "runtime parameter for tool Design primers to features", |
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Uploaded CAPS marker design workflow for 454 Data
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316 "name": "min_size" |
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Uploaded CAPS marker design workflow for 454 Data
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317 }, |
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Uploaded CAPS marker design workflow for 454 Data
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318 { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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319 "description": "runtime parameter for tool Design primers to features", |
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Uploaded CAPS marker design workflow for 454 Data
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320 "name": "max_size" |
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321 } |
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Uploaded CAPS marker design workflow for 454 Data
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322 ], |
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Uploaded CAPS marker design workflow for 454 Data
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323 "name": "Design primers to features", |
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Uploaded CAPS marker design workflow for 454 Data
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324 "outputs": [ |
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Uploaded CAPS marker design workflow for 454 Data
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325 { |
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Uploaded CAPS marker design workflow for 454 Data
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326 "name": "primer_outputfile", |
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327 "type": "tabular" |
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Uploaded CAPS marker design workflow for 454 Data
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328 } |
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Uploaded CAPS marker design workflow for 454 Data
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329 ], |
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Uploaded CAPS marker design workflow for 454 Data
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330 "position": { |
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Uploaded CAPS marker design workflow for 454 Data
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334 "post_job_actions": {}, |
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335 "tool_errors": null, |
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336 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0", |
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337 "tool_state": "{\"__page__\": 0, \"inputTargetfile\": \"null\", \"inputfastaFile\": \"null\", \"min_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputSNPfile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"max_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", |
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338 "tool_version": "1.0.0", |
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339 "type": "tool", |
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Uploaded CAPS marker design workflow for 454 Data
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340 "user_outputs": [] |
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341 }, |
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Uploaded CAPS marker design workflow for 454 Data
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342 "8": { |
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Uploaded CAPS marker design workflow for 454 Data
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343 "annotation": "Select successful design targets", |
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Uploaded CAPS marker design workflow for 454 Data
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344 "id": 8, |
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345 "input_connections": { |
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346 "input": { |
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347 "id": 7, |
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348 "output_name": "primer_outputfile" |
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Uploaded CAPS marker design workflow for 454 Data
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349 } |
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Uploaded CAPS marker design workflow for 454 Data
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350 }, |
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Uploaded CAPS marker design workflow for 454 Data
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351 "inputs": [], |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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352 "name": "Select", |
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353 "outputs": [ |
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354 { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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355 "name": "out_file1", |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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356 "type": "input" |
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Uploaded CAPS marker design workflow for 454 Data
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357 } |
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Uploaded CAPS marker design workflow for 454 Data
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358 ], |
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Uploaded CAPS marker design workflow for 454 Data
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359 "position": { |
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Uploaded CAPS marker design workflow for 454 Data
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Uploaded CAPS marker design workflow for 454 Data
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Uploaded CAPS marker design workflow for 454 Data
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362 }, |
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Uploaded CAPS marker design workflow for 454 Data
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363 "post_job_actions": {}, |
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Uploaded CAPS marker design workflow for 454 Data
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364 "tool_errors": null, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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365 "tool_id": "Grep1", |
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366 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"NONE\\\"\"}", |
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john-mccallum
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367 "tool_version": "1.0.1", |
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john-mccallum
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368 "type": "tool", |
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369 "user_outputs": [] |
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Uploaded CAPS marker design workflow for 454 Data
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370 }, |
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Uploaded CAPS marker design workflow for 454 Data
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371 "9": { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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372 "annotation": "Remove duplicates", |
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Uploaded CAPS marker design workflow for 454 Data
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373 "id": 9, |
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374 "input_connections": { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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375 "inputFile": { |
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376 "id": 8, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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377 "output_name": "out_file1" |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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378 } |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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379 }, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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380 "inputs": [], |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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381 "name": "Unique", |
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Uploaded CAPS marker design workflow for 454 Data
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382 "outputs": [ |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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383 { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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384 "name": "outputfile", |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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385 "type": "txt" |
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386 } |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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387 ], |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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388 "position": { |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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389 "left": 1900.6818237304688, |
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Uploaded CAPS marker design workflow for 454 Data
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390 "top": 310.90907287597656 |
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Uploaded CAPS marker design workflow for 454 Data
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391 }, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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392 "post_job_actions": {}, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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393 "tool_errors": null, |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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394 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0", |
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Uploaded CAPS marker design workflow for 454 Data
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395 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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396 "tool_version": "1.0.0", |
ea2117a7b363
Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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397 "type": "tool", |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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398 "user_outputs": [] |
ea2117a7b363
Uploaded CAPS marker design workflow for 454 Data
john-mccallum
parents:
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399 } |
ea2117a7b363
Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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400 } |
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Uploaded CAPS marker design workflow for 454 Data
john-mccallum
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401 } |