annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga @ 2:48b020a0d2f7 draft

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date Fri, 13 May 2016 05:46:40 -0400
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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93 {
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94 "name": "output_aligned_reads_r",
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96 },
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97 {
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98 "name": "output_unaligned_reads_r",
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99 "type": "fastqsanger"
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100 },
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101 {
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102 "name": "output",
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103 "type": "bam"
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104 },
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105 {
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106 "name": "output_sam",
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107 "type": "sam"
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108 },
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109 {
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110 "name": "mapping_stats",
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111 "type": "txt"
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112 }
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113 ],
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114 "position": {
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117 },
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118 "post_job_actions": {
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119 "DeleteIntermediatesActionoutput_unaligned_reads_l": {
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120 "action_arguments": {},
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121 "action_type": "DeleteIntermediatesAction",
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122 "output_name": "output_unaligned_reads_l"
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123 },
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124 "HideDatasetActionmapping_stats": {
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125 "action_arguments": {},
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126 "action_type": "HideDatasetAction",
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127 "output_name": "mapping_stats"
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128 },
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129 "HideDatasetActionoutput": {
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130 "action_arguments": {},
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131 "action_type": "HideDatasetAction",
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132 "output_name": "output"
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133 },
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134 "HideDatasetActionoutput_aligned_reads_r": {
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135 "action_arguments": {},
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136 "action_type": "HideDatasetAction",
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137 "output_name": "output_aligned_reads_r"
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138 },
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139 "HideDatasetActionoutput_sam": {
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140 "action_arguments": {},
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141 "action_type": "HideDatasetAction",
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142 "output_name": "output_sam"
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143 },
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144 "HideDatasetActionoutput_unaligned_reads_l": {
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145 "action_arguments": {},
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146 "action_type": "HideDatasetAction",
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147 "output_name": "output_unaligned_reads_l"
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148 },
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149 "HideDatasetActionoutput_unaligned_reads_r": {
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150 "action_arguments": {},
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151 "action_type": "HideDatasetAction",
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152 "output_name": "output_unaligned_reads_r"
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153 }
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154 },
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155 "tool_errors": null,
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156 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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157 "tool_shed_repository": {
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158 "changeset_revision": "a9d4f71dbfb0",
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159 "name": "bowtie2",
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160 "owner": "devteam",
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161 "tool_shed": "toolshed.g2.bx.psu.edu"
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162 },
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163 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg19\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}",
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164 "tool_version": "2.2.6.2",
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165 "type": "tool",
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166 "uuid": "76fe9f4e-cf0b-4480-aadf-ba461c595414",
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167 "workflow_outputs": [
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168 {
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169 "label": null,
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170 "output_name": "output_aligned_reads_l",
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171 "uuid": "ec776ac8-cd59-4d76-9ad8-d82905393ad7"
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172 }
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173 ]
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174 },
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175 "3": {
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176 "annotation": "",
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177 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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178 "id": 3,
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179 "input_connections": {
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180 "library|input_1": {
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181 "id": 2,
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182 "output_name": "output_unaligned_reads_l"
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183 }
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184 },
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185 "inputs": [],
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186 "label": null,
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187 "name": "Bowtie2",
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188 "outputs": [
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189 {
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190 "name": "output_unaligned_reads_l",
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191 "type": "fastqsanger"
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192 },
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193 {
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194 "name": "output_aligned_reads_l",
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195 "type": "fastqsanger"
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196 },
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197 {
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198 "name": "output_aligned_reads_r",
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199 "type": "fastqsanger"
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200 },
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201 {
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202 "name": "output_unaligned_reads_r",
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203 "type": "fastqsanger"
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204 },
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205 {
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206 "name": "output",
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207 "type": "bam"
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208 },
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209 {
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210 "name": "output_sam",
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211 "type": "sam"
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212 },
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213 {
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214 "name": "mapping_stats",
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215 "type": "txt"
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216 }
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217 ],
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218 "position": {
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221 },
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223 "ChangeDatatypeActionoutput_sam": {
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224 "action_arguments": {
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225 "newtype": "tabular"
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226 },
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227 "action_type": "ChangeDatatypeAction",
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228 "output_name": "output_sam"
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229 },
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230 "DeleteIntermediatesActionoutput_unaligned_reads_l": {
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231 "action_arguments": {},
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232 "action_type": "DeleteIntermediatesAction",
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233 "output_name": "output_unaligned_reads_l"
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234 },
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235 "HideDatasetActionmapping_stats": {
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236 "action_arguments": {},
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237 "action_type": "HideDatasetAction",
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238 "output_name": "mapping_stats"
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239 },
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240 "HideDatasetActionoutput": {
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241 "action_arguments": {},
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242 "action_type": "HideDatasetAction",
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243 "output_name": "output"
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244 },
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245 "HideDatasetActionoutput_aligned_reads_r": {
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246 "action_arguments": {},
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247 "action_type": "HideDatasetAction",
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248 "output_name": "output_aligned_reads_r"
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249 },
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250 "HideDatasetActionoutput_sam": {
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251 "action_arguments": {},
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252 "action_type": "HideDatasetAction",
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253 "output_name": "output_sam"
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254 },
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255 "HideDatasetActionoutput_unaligned_reads_l": {
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256 "action_arguments": {},
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257 "action_type": "HideDatasetAction",
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258 "output_name": "output_unaligned_reads_l"
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259 },
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260 "HideDatasetActionoutput_unaligned_reads_r": {
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261 "action_arguments": {},
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262 "action_type": "HideDatasetAction",
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263 "output_name": "output_unaligned_reads_r"
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264 }
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265 },
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266 "tool_errors": null,
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267 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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268 "tool_shed_repository": {
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269 "changeset_revision": "a9d4f71dbfb0",
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270 "name": "bowtie2",
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271 "owner": "devteam",
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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627 {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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628 "label": null,
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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629 "output_name": "out_file1",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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630 "uuid": "a177238a-37d7-469b-a243-1330acc04024"
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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631 }
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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632 ]
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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633 }
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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634 },
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3d8eb2c065c7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit a143c96a3168e4135202479cb58e5a2bcdd153b4
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635 "uuid": "e478bbdb-f34d-48f4-9cb6-b54be280f669"
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4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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636 }