annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga @ 1:3d8eb2c065c7 draft

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author drosofff
date Mon, 11 Apr 2016 13:14:14 -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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95 "type": "fastqsanger"
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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 {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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102 "name": "output",
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103 "type": "bam"
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104 },
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105 {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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 {
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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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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115 "left": 426.5625,
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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_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\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"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}}\"}",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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158 "tool_version": "2.2.6.2",
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159 "type": "tool",
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160 "uuid": "76fe9f4e-cf0b-4480-aadf-ba461c595414",
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161 "workflow_outputs": [
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162 {
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163 "label": null,
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164 "output_name": "output_aligned_reads_l",
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165 "uuid": "ec776ac8-cd59-4d76-9ad8-d82905393ad7"
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166 }
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167 ]
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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168 },
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169 "3": {
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170 "annotation": "",
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171 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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172 "id": 3,
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173 "input_connections": {
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174 "library|input_1": {
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175 "id": 2,
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176 "output_name": "output_unaligned_reads_l"
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177 }
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178 },
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179 "inputs": [],
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180 "label": null,
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181 "name": "Bowtie2",
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182 "outputs": [
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183 {
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184 "name": "output_unaligned_reads_l",
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185 "type": "fastqsanger"
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186 },
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187 {
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188 "name": "output_aligned_reads_l",
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189 "type": "fastqsanger"
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190 },
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191 {
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192 "name": "output_aligned_reads_r",
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193 "type": "fastqsanger"
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194 },
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195 {
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196 "name": "output_unaligned_reads_r",
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197 "type": "fastqsanger"
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198 },
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199 {
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200 "name": "output",
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201 "type": "bam"
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202 },
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203 {
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204 "name": "output_sam",
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205 "type": "sam"
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206 },
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207 {
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208 "name": "mapping_stats",
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209 "type": "txt"
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210 }
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211 ],
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212 "position": {
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213 "left": 776.53125,
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215 },
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216 "post_job_actions": {
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217 "ChangeDatatypeActionoutput_sam": {
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218 "action_arguments": {
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219 "newtype": "tabular"
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220 },
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221 "action_type": "ChangeDatatypeAction",
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222 "output_name": "output_sam"
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223 },
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224 "DeleteIntermediatesActionoutput_unaligned_reads_l": {
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225 "action_arguments": {},
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226 "action_type": "DeleteIntermediatesAction",
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227 "output_name": "output_unaligned_reads_l"
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228 },
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229 "HideDatasetActionmapping_stats": {
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230 "action_arguments": {},
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231 "action_type": "HideDatasetAction",
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232 "output_name": "mapping_stats"
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233 },
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234 "HideDatasetActionoutput": {
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235 "action_arguments": {},
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236 "action_type": "HideDatasetAction",
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237 "output_name": "output"
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238 },
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239 "HideDatasetActionoutput_aligned_reads_r": {
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240 "action_arguments": {},
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241 "action_type": "HideDatasetAction",
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242 "output_name": "output_aligned_reads_r"
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243 },
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244 "HideDatasetActionoutput_sam": {
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245 "action_arguments": {},
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246 "action_type": "HideDatasetAction",
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247 "output_name": "output_sam"
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248 },
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249 "HideDatasetActionoutput_unaligned_reads_l": {
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250 "action_arguments": {},
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251 "action_type": "HideDatasetAction",
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252 "output_name": "output_unaligned_reads_l"
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253 },
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254 "HideDatasetActionoutput_unaligned_reads_r": {
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255 "action_arguments": {},
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256 "action_type": "HideDatasetAction",
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257 "output_name": "output_unaligned_reads_r"
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258 }
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259 },
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260 "tool_errors": null,
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261 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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262 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"True\\\", \\\"unaligned_file\\\": \\\"False\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"vir1\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"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}}\"}",
4a47903bb4df planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209
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263 "tool_version": "2.2.6.2",
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264 "type": "tool",
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265 "uuid": "5f6b3d0e-06eb-4e75-9139-b41a4d88f79a",
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266 "workflow_outputs": [
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267 {
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