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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "MMuFLR_Human_v1.4",
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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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21 "top": 314
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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": 410
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45 },
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46 "tool_errors": null,
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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": 2362,
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67 "top": 745
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68 },
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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": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)",
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78 "id": 3,
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79 "input_connections": {},
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80 "inputs": [
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81 {
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82 "description": "These are locations other than those in dbSNP. This could include variants from the subject normal tissue. \nThe ID will be used to annotate the Variants dataset, and then can be filtered out. There needs to be at least one entry for each chromosome: (M,1,2,...,X,Y)",
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83 "name": "VCF file of additional known variants "
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84 }
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85 ],
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86 "name": "Input dataset",
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87 "outputs": [],
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88 "position": {
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89 "left": 4388,
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90 "top": 576
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91 },
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95 "tool_version": null,
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96 "type": "data_input",
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97 "user_outputs": []
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98 },
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99 "4": {
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100 "annotation": "Convert quality scores to sanger scale",
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101 "id": 4,
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102 "input_connections": {
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103 "input_file": {
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104 "id": 0,
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105 "output_name": "output"
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106 }
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107 },
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108 "inputs": [
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109 {
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110 "description": "runtime parameter for tool FASTQ Groomer",
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111 "name": "input_type"
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112 }
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113 ],
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114 "name": "FASTQ Groomer",
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115 "outputs": [
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116 {
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117 "name": "output_file",
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118 "type": "fastqsanger"
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130 "type": "tool",
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131 "user_outputs": []
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132 },
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133 "5": {
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135 "id": 5,
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136 "input_connections": {
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137 "input_file": {
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138 "id": 1,
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139 "output_name": "output"
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140 }
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141 },
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142 "inputs": [
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143 {
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144 "description": "runtime parameter for tool FASTQ Groomer",
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145 "name": "input_type"
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146 }
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147 ],
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148 "name": "FASTQ Groomer",
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149 "outputs": [
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150 {
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151 "name": "output_file",
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152 "type": "fastqsanger"
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153 }
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154 ],
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155 "position": {
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157 "top": 431
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163 "tool_version": "1.0.4",
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165 "user_outputs": []
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166 },
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167 "6": {
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168 "annotation": "Map paired reads to reference genome",
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169 "id": 6,
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170 "input_connections": {
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171 "input1": {
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173 "output_name": "output_file"
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174 },
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175 "singlePaired|input2": {
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176 "id": 5,
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177 "output_name": "output_file"
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178 }
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179 },
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180 "inputs": [
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181 {
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182 "description": "runtime parameter for tool Tophat for Illumina",
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183 "name": "singlePaired"
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184 }
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185 ],
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186 "name": "Tophat for Illumina",
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187 "outputs": [
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188 {
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189 "name": "insertions",
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190 "type": "bed"
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191 },
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192 {
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193 "name": "deletions",
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194 "type": "bed"
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195 },
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196 {
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197 "name": "junctions",
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198 "type": "bed"
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199 },
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200 {
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201 "name": "accepted_hits",
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202 "type": "bam"
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203 }
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204 ],
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205 "position": {
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206 "left": 884,
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209 "post_job_actions": {
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210 "HideDatasetActiondeletions": {
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211 "action_arguments": {},
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212 "action_type": "HideDatasetAction",
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213 "output_name": "deletions"
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214 },
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215 "HideDatasetActioninsertions": {
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217 "action_type": "HideDatasetAction",
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218 "output_name": "insertions"
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221 "action_arguments": {},
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222 "action_type": "HideDatasetAction",
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223 "output_name": "junctions"
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224 }
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225 },
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226 "tool_errors": null,
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227 "tool_id": "tophat",
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228 "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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"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\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}",
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229 "tool_version": "1.5.0",
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230 "type": "tool",
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231 "user_outputs": []
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232 },
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233 "7": {
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234 "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)",
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235 "id": 7,
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236 "input_connections": {
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237 "input1": {
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238 "id": 6,
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239 "output_name": "accepted_hits"
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240 }
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241 },
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242 "inputs": [],
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243 "name": "Filter SAM or BAM",
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244 "outputs": [
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245 {
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246 "name": "output1",
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247 "type": "sam"
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248 }
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249 ],
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250 "position": {
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251 "left": 1154,
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252 "top": 366
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253 },
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254 "post_job_actions": {
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255 "HideDatasetActionoutput1": {
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256 "action_arguments": {},
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257 "action_type": "HideDatasetAction",
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258 "output_name": "output1"
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259 }
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260 },
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261 "tool_errors": null,
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262 "tool_id": "samtools_filter",
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273 "id": 7,
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274 "output_name": "output1"
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275 }
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276 },
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277 "inputs": [],
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278 "name": "flagstat",
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279 "outputs": [
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280 {
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281 "name": "output1",
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282 "type": "txt"
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283 }
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287 "top": 323
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289 "post_job_actions": {},
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293 "tool_version": "1.0.0",
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294 "type": "tool",
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295 "user_outputs": []
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296 },
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297 "9": {
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298 "annotation": "Add Read Group info required by GATK tools",
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299 "id": 9,
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300 "input_connections": {
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301 "inputFile": {
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302 "id": 7,
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303 "output_name": "output1"
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304 }
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305 },
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306 "inputs": [],
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307 "name": "Add or Replace Groups",
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308 "outputs": [
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309 {
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310 "name": "outFile",
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311 "type": "bam"
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312 }
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314 "position": {
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315 "left": 1506,
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316 "top": 503
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317 },
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318 "post_job_actions": {},
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319 "tool_errors": null,
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320 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0",
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322 "tool_version": "1.56.0",
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323 "type": "tool",
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324 "user_outputs": []
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325 },
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326 "10": {
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327 "annotation": "Synchronize paired reads",
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328 "id": 10,
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329 "input_connections": {
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330 "input_file": {
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332 "output_name": "outFile"
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333 }
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334 },
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335 "inputs": [],
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336 "name": "Paired Read Mate Fixer",
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337 "outputs": [
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338 {
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339 "name": "out_file",
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340 "type": "bam"
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341 }
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342 ],
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343 "position": {
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344 "left": 1841,
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345 "top": 375
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346 },
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347 "post_job_actions": {
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348 "HideDatasetActionout_file": {
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349 "action_arguments": {},
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350 "action_type": "HideDatasetAction",
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351 "output_name": "out_file"
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352 }
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353 },
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354 "tool_errors": null,
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355 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0",
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356 "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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357 "tool_version": "1.56.0",
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358 "type": "tool",
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359 "user_outputs": []
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360 },
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361 "11": {
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362 "annotation": "Remove duplicate reads",
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363 "id": 11,
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364 "input_connections": {
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365 "input_file": {
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366 "id": 10,
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367 "output_name": "out_file"
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368 }
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369 },
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370 "inputs": [],
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371 "name": "Mark Duplicate reads",
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372 "outputs": [
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373 {
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374 "name": "out_file",
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375 "type": "bam"
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376 },
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377 {
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378 "name": "html_file",
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379 "type": "html"
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380 }
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381 ],
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382 "position": {
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383 "left": 2086,
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384 "top": 360
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