Mercurial > repos > jjohnson > mmuff
annotate Galaxy-Workflow-MMuFF_Human_germline_v1.2.ga @ 6:2aa99b7f90f4 draft default tip
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author | jjohnson |
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date | Thu, 30 May 2013 11:27:21 -0400 |
parents | 04e170c09922 |
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Add a workflow for noraml tissue samples.
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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": "MMuFF_Human_germline_v1.2", |
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6 "steps": { |
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7 "0": { |
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8 "annotation": "Human RNA-seq paired reads left mates", |
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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": "Human RNA-seq paired reads left mates", |
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14 "name": "Forward reads 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": 240, |
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21 "top": 287 |
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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\": \"Forward reads 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": "Human RNA-seq paired reads right mates", |
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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": "Human RNA-seq paired reads right mates", |
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37 "name": "Reverse reads fastq" |
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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": 249, |
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44 "top": 383 |
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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\": \"Reverse reads fastq\"}", |
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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": "Known SNPs - dbSNP.vcf", |
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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": "Known SNPs - dbSNP.vcf", |
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60 "name": "VCF file of known variants (dbSNP)" |
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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": 2327, |
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67 "top": 758 |
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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\": \"VCF file of known variants (dbSNP)\"}", |
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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": "Convert quality scores to sanger scale", |
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78 "id": 3, |
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79 "input_connections": { |
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80 "input_file": { |
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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 { |
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87 "description": "runtime parameter for tool FASTQ Groomer", |
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88 "name": "input_type" |
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89 } |
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90 ], |
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91 "name": "FASTQ Groomer", |
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92 "outputs": [ |
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93 { |
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94 "name": "output_file", |
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95 "type": "fastqsanger" |
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96 } |
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97 ], |
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98 "position": { |
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99 "left": 510, |
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100 "top": 264 |
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101 }, |
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102 "post_job_actions": {}, |
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103 "tool_errors": null, |
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104 "tool_id": "fastq_groomer", |
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105 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", |
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106 "tool_version": "1.0.4", |
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107 "type": "tool", |
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108 "user_outputs": [] |
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109 }, |
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110 "4": { |
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111 "annotation": "Convert quality scores to sanger scale", |
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112 "id": 4, |
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113 "input_connections": { |
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114 "input_file": { |
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115 "id": 1, |
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116 "output_name": "output" |
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117 } |
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118 }, |
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119 "inputs": [ |
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120 { |
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121 "description": "runtime parameter for tool FASTQ Groomer", |
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122 "name": "input_type" |
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123 } |
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124 ], |
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125 "name": "FASTQ Groomer", |
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126 "outputs": [ |
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127 { |
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128 "name": "output_file", |
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129 "type": "fastqsanger" |
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130 } |
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131 ], |
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132 "position": { |
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133 "left": 505, |
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134 "top": 404 |
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135 }, |
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136 "post_job_actions": {}, |
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137 "tool_errors": null, |
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138 "tool_id": "fastq_groomer", |
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139 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", |
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140 "tool_version": "1.0.4", |
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141 "type": "tool", |
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142 "user_outputs": [] |
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143 }, |
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144 "5": { |
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145 "annotation": "Map paired reads to reference genome", |
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146 "id": 5, |
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147 "input_connections": { |
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148 "input1": { |
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149 "id": 3, |
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150 "output_name": "output_file" |
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151 }, |
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152 "singlePaired|input2": { |
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153 "id": 4, |
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154 "output_name": "output_file" |
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155 } |
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156 }, |
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157 "inputs": [], |
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158 "name": "Tophat for Illumina", |
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159 "outputs": [ |
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160 { |
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161 "name": "insertions", |
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162 "type": "bed" |
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163 }, |
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164 { |
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165 "name": "deletions", |
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166 "type": "bed" |
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167 }, |
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168 { |
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169 "name": "junctions", |
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170 "type": "bed" |
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171 }, |
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172 { |
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173 "name": "accepted_hits", |
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174 "type": "bam" |
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175 } |
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176 ], |
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177 "position": { |
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178 "left": 884, |
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179 "top": 305 |
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180 }, |
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181 "post_job_actions": { |
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182 "HideDatasetActiondeletions": { |
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183 "action_arguments": {}, |
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184 "action_type": "HideDatasetAction", |
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185 "output_name": "deletions" |
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186 }, |
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187 "HideDatasetActioninsertions": { |
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188 "action_arguments": {}, |
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189 "action_type": "HideDatasetAction", |
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190 "output_name": "insertions" |
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191 }, |
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192 "HideDatasetActionjunctions": { |
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193 "action_arguments": {}, |
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194 "action_type": "HideDatasetAction", |
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195 "output_name": "junctions" |
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196 } |
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197 }, |
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198 "tool_errors": null, |
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199 "tool_id": "tophat", |
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200 "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"80\\\"}\"}", |
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201 "tool_version": "1.5.0", |
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202 "type": "tool", |
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203 "user_outputs": [] |
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204 }, |
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205 "6": { |
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206 "annotation": "Keep only mappings with MAPQ of 255", |
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207 "id": 6, |
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208 "input_connections": { |
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209 "input1": { |
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210 "id": 5, |
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211 "output_name": "accepted_hits" |
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212 } |
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213 }, |
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214 "inputs": [], |
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215 "name": "Filter SAM or BAM", |
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216 "outputs": [ |
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217 { |
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218 "name": "output1", |
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219 "type": "sam" |
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220 } |
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221 ], |
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222 "position": { |
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223 "left": 1154, |
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224 "top": 339 |
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225 }, |
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226 "post_job_actions": { |
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227 "HideDatasetActionoutput1": { |
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228 "action_arguments": {}, |
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229 "action_type": "HideDatasetAction", |
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230 "output_name": "output1" |
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231 } |
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232 }, |
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233 "tool_errors": null, |
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234 "tool_id": "samtools_filter", |
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235 "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", |
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236 "tool_version": "1.1.0", |
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237 "type": "tool", |
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238 "user_outputs": [] |
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239 }, |
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240 "7": { |
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241 "annotation": "", |
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242 "id": 7, |
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243 "input_connections": { |
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244 "input1": { |
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245 "id": 6, |
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246 "output_name": "output1" |
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247 } |
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248 }, |
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249 "inputs": [], |
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250 "name": "flagstat", |
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251 "outputs": [ |
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252 { |
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253 "name": "output1", |
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254 "type": "txt" |
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255 } |
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256 ], |
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257 "position": { |
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258 "left": 1505, |
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259 "top": 296 |
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260 }, |
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261 "post_job_actions": {}, |
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262 "tool_errors": null, |
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263 "tool_id": "samtools_flagstat", |
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264 "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", |
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265 "tool_version": "1.0.0", |
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266 "type": "tool", |
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267 "user_outputs": [] |
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268 }, |
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269 "8": { |
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270 "annotation": "Add Read Group info required by GATK tools", |
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271 "id": 8, |
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272 "input_connections": { |
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273 "inputFile": { |
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274 "id": 6, |
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275 "output_name": "output1" |
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276 } |
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277 }, |
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278 "inputs": [], |
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279 "name": "Add or Replace Groups", |
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280 "outputs": [ |
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281 { |
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282 "name": "outFile", |
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283 "type": "bam" |
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284 } |
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285 ], |
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286 "position": { |
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287 "left": 1506, |
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288 "top": 476 |
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289 }, |
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290 "post_job_actions": {}, |
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291 "tool_errors": null, |
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292 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", |
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293 "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", |
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294 "tool_version": "1.56.0", |
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295 "type": "tool", |
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296 "user_outputs": [] |
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297 }, |
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298 "9": { |
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299 "annotation": "Synchronize paired reads", |
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300 "id": 9, |
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301 "input_connections": { |
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302 "input_file": { |
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303 "id": 8, |
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304 "output_name": "outFile" |
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305 } |
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306 }, |
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307 "inputs": [], |
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308 "name": "Paired Read Mate Fixer", |
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309 "outputs": [ |
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310 { |
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311 "name": "out_file", |
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312 "type": "bam" |
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313 } |
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314 ], |
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315 "position": { |
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316 "left": 1841, |
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317 "top": 348 |
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318 }, |
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319 "post_job_actions": { |
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320 "HideDatasetActionout_file": { |
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321 "action_arguments": {}, |
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322 "action_type": "HideDatasetAction", |
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323 "output_name": "out_file" |
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324 } |
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325 }, |
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326 "tool_errors": null, |
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327 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", |
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328 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", |
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329 "tool_version": "1.56.0", |
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330 "type": "tool", |
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331 "user_outputs": [] |
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332 }, |
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333 "10": { |
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334 "annotation": "Remove duplicate reads", |
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335 "id": 10, |
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336 "input_connections": { |
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337 "input_file": { |
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338 "id": 9, |
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339 "output_name": "out_file" |
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340 } |
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341 }, |
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342 "inputs": [], |
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343 "name": "Mark Duplicate reads", |
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344 "outputs": [ |
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345 { |
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346 "name": "out_file", |
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347 "type": "bam" |
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348 }, |
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349 { |
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350 "name": "html_file", |
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351 "type": "html" |
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352 } |
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353 ], |
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354 "position": { |
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355 "left": 2086, |
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356 "top": 333 |
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357 }, |
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358 "post_job_actions": {}, |
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359 "tool_errors": null, |
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360 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", |
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361 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", |
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362 "tool_version": "1.56.0", |
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363 "type": "tool", |
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364 "user_outputs": [] |
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365 }, |
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366 "11": { |
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367 "annotation": "Reorder BAM for GATK tools", |
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368 "id": 11, |
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369 "input_connections": { |
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370 "inputFile": { |
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371 "id": 10, |
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372 "output_name": "out_file" |
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373 } |
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374 }, |
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375 "inputs": [], |
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376 "name": "Reorder SAM/BAM", |
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377 "outputs": [ |
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378 { |
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379 "name": "outFile", |
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380 "type": "bam" |
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381 } |
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382 ], |
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383 "position": { |
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384 "left": 2401, |
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385 "top": 305 |
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386 }, |
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387 "post_job_actions": {}, |
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388 "tool_errors": null, |
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389 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", |
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390 "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", |
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391 "tool_version": "1.56.0", |
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392 "type": "tool", |
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393 "user_outputs": [] |
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394 }, |
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395 "12": { |
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396 "annotation": "", |
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397 "id": 12, |
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398 "input_connections": { |
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399 "reference_source|input_bam": { |
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400 "id": 11, |
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401 "output_name": "outFile" |
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402 }, |
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403 "rod_bind_0|rod_bind_type|input_rod": { |
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404 "id": 2, |
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405 "output_name": "output" |
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406 } |
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407 }, |
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408 "inputs": [], |
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409 "name": "Realigner Target Creator", |
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410 "outputs": [ |
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411 { |
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412 "name": "output_interval", |
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413 "type": "gatk_interval" |
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414 }, |
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415 { |
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416 "name": "output_log", |
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417 "type": "txt" |
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418 } |
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419 ], |
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420 "position": { |
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421 "left": 2565, |
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422 "top": 491 |
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423 }, |
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424 "post_job_actions": { |
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425 "HideDatasetActionoutput_log": { |
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426 "action_arguments": {}, |
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Add a workflow for noraml tissue samples.
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parents:
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427 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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428 "output_name": "output_log" |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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429 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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430 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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431 "tool_errors": null, |
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parents:
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432 "tool_id": "gatk_realigner_target_creator", |
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Add a workflow for noraml tissue samples.
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433 "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", |
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Add a workflow for noraml tissue samples.
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434 "tool_version": "0.0.4", |
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Jim Johnson <jj@umn.edu>
parents:
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435 "type": "tool", |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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436 "user_outputs": [] |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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437 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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438 "13": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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439 "annotation": "Perform local realignments for indels", |
04e170c09922
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Jim Johnson <jj@umn.edu>
parents:
diff
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440 "id": 13, |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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441 "input_connections": { |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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442 "reference_source|input_bam": { |
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Jim Johnson <jj@umn.edu>
parents:
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443 "id": 11, |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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444 "output_name": "outFile" |
04e170c09922
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Jim Johnson <jj@umn.edu>
parents:
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445 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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446 "target_intervals": { |
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Jim Johnson <jj@umn.edu>
parents:
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447 "id": 12, |
04e170c09922
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Jim Johnson <jj@umn.edu>
parents:
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448 "output_name": "output_interval" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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449 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
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450 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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451 "inputs": [], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
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452 "name": "Indel Realigner", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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453 "outputs": [ |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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changeset
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454 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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455 "name": "output_bam", |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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456 "type": "bam" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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457 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
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458 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
459 "name": "output_log", |
04e170c09922
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Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
460 "type": "txt" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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461 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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462 ], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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463 "position": { |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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464 "left": 2811, |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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465 "top": 324 |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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466 }, |
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Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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467 "post_job_actions": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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468 "HideDatasetActionoutput_log": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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469 "action_arguments": {}, |
04e170c09922
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Jim Johnson <jj@umn.edu>
parents:
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470 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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|
471 "output_name": "output_log" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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472 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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473 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
474 "tool_errors": null, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
475 "tool_id": "gatk_indel_realigner", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
476 "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", |
04e170c09922
Add a workflow for noraml tissue samples.
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parents:
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477 "tool_version": "0.0.6", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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478 "type": "tool", |
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Jim Johnson <jj@umn.edu>
parents:
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479 "user_outputs": [] |
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Jim Johnson <jj@umn.edu>
parents:
diff
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480 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
481 "14": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
482 "annotation": "Check again for duplicate reads and eliminate", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
483 "id": 14, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
484 "input_connections": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
485 "input_file": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
486 "id": 13, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
487 "output_name": "output_bam" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
488 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
489 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
490 "inputs": [], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
491 "name": "Mark Duplicate reads", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
492 "outputs": [ |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
493 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
494 "name": "out_file", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
495 "type": "bam" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
496 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
497 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
498 "name": "html_file", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
499 "type": "html" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
500 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
501 ], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
502 "position": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
503 "left": 3174, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
504 "top": 291 |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
505 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
506 "post_job_actions": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
507 "HideDatasetActionhtml_file": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
508 "action_arguments": {}, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
509 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
510 "output_name": "html_file" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
511 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
512 "HideDatasetActionout_file": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
513 "action_arguments": {}, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
514 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
515 "output_name": "out_file" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
516 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
517 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
518 "tool_errors": null, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
519 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
520 "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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|
521 "tool_version": "1.56.0", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
522 "type": "tool", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
523 "user_outputs": [] |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
524 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
525 "15": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
526 "annotation": "Determine base calls at each position", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
527 "id": 15, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
528 "input_connections": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
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|
529 "reference_source|input_bams_0|input_bam": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
530 "id": 14, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
531 "output_name": "out_file" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
532 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
533 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
534 "inputs": [], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
535 "name": "MPileup", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
536 "outputs": [ |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
537 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
538 "name": "output_mpileup", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
539 "type": "pileup" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
540 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
541 { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
542 "name": "output_log", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
543 "type": "txt" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
544 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
545 ], |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
546 "position": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
547 "left": 3554, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
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548 "top": 265 |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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|
549 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
550 "post_job_actions": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
551 "HideDatasetActionoutput_log": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
552 "action_arguments": {}, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
553 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
554 "output_name": "output_log" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
555 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
556 "HideDatasetActionoutput_mpileup": { |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
557 "action_arguments": {}, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
558 "action_type": "HideDatasetAction", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
559 "output_name": "output_mpileup" |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
560 } |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
561 }, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
562 "tool_errors": null, |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
563 "tool_id": "samtools_mpileup", |
04e170c09922
Add a workflow for noraml tissue samples.
Jim Johnson <jj@umn.edu>
parents:
diff
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564 "tool_state": "{\"__page__\": 0, \"advanced_options\": \"{\\\"max_reads_per_bam\\\": \\\"2500\\\", \\\"advanced_options_selector\\\": \\\"advanced\\\", \\\"extended_BAQ_computation\\\": \\\"False\\\", \\\"region_string\\\": \\\"\\\", \\\"output_per_sample_strand_bias_p_value\\\": \\\"False\\\", \\\"minimum_base_quality\\\": \\\"20\\\", \\\"disable_probabilistic_realignment\\\": \\\"True\\\", \\\"skip_anomalous_read_pairs\\\": \\\"True\\\", \\\"minimum_mapping_quality\\\": \\\"0\\\", \\\"output_per_sample_read_depth\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"position_list\\\": null, \\\"coefficient_for_downgrading\\\": \\\"0\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"genotype_likelihood_computation_type\": \"{\\\"genotype_likelihood_computation_type_selector\\\": \\\"do_not_perform_genotype_likelihood_computation\\\", \\\"__current_case__\\\": 1}\", \"reference_source\": \"{\\\"ref_file\\\": \\\"hg19_canonical\\\", \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bams\\\": [{\\\"__index__\\\": 0, \\\"input_bam\\\": null}], \\\"__current_case__\\\": 0}\"}", |
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565 "tool_version": "0.0.1", |
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566 "type": "tool", |
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567 "user_outputs": [] |
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568 }, |
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569 "16": { |
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570 "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele: .33\nVCF_ID = germline", |
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571 "id": 16, |
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572 "input_connections": { |
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573 "input_file": { |
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574 "id": 15, |
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575 "output_name": "output_mpileup" |
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576 } |
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577 }, |
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578 "inputs": [ |
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579 { |
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580 "description": "runtime parameter for tool Pileup to VCF", |
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581 "name": "min_base_qual" |
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582 } |
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583 ], |
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584 "name": "Pileup to VCF", |
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585 "outputs": [ |
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586 { |
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587 "name": "output_file", |
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588 "type": "vcf" |
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589 } |
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590 ], |
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591 "position": { |
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592 "left": 3937, |
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593 "top": 258 |
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594 }, |
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595 "post_job_actions": {}, |
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596 "tool_errors": null, |
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597 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/pileup_to_vcf/pileup_to_vcf/2.0", |
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598 "tool_state": "{\"snps_only\": \"\\\"False\\\"\", \"min_cvrg\": \"\\\"5\\\"\", \"allow_multiples\": \"\\\"True\\\"\", \"input_file\": \"null\", \"__page__\": 0, \"vcf_id\": \"\\\"germline\\\"\", \"cols\": \"{\\\"select_order\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"depth_as\": \"\\\"ref\\\"\", \"min_base_qual\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min_var_pct\": \"\\\"0.33\\\"\"}", |
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599 "tool_version": "2.2", |
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600 "type": "tool", |
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601 "user_outputs": [] |
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602 } |
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603 } |
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604 } |