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96 "type": "fastqsanger"
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97 },
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98 {
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99 "name": "output_aligned_reads_r",
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100 "type": "fastqsanger"
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101 },
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102 {
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103 "name": "output_unaligned_reads_r",
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104 "type": "fastqsanger"
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105 },
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106 {
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107 "name": "output",
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108 "type": "bam"
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109 },
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110 {
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111 "name": "output_sam",
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112 "type": "sam"
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113 },
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114 {
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115 "name": "mapping_stats",
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116 "type": "txt"
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117 }
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118 ],
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119 "position": {
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120 "left": 462.484375,
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122 },
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123 "post_job_actions": {
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124 "DeleteIntermediatesActionoutput_unaligned_reads_l": {
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125 "action_arguments": {},
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126 "action_type": "DeleteIntermediatesAction",
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127 "output_name": "output_unaligned_reads_l"
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128 },
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129 "HideDatasetActionmapping_stats": {
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130 "action_arguments": {},
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131 "action_type": "HideDatasetAction",
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132 "output_name": "mapping_stats"
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133 },
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134 "HideDatasetActionoutput": {
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135 "action_arguments": {},
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136 "action_type": "HideDatasetAction",
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137 "output_name": "output"
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138 },
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139 "HideDatasetActionoutput_aligned_reads_l": {
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140 "action_arguments": {},
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141 "action_type": "HideDatasetAction",
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142 "output_name": "output_aligned_reads_l"
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143 },
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144 "HideDatasetActionoutput_aligned_reads_r": {
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145 "action_arguments": {},
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146 "action_type": "HideDatasetAction",
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147 "output_name": "output_aligned_reads_r"
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148 },
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149 "HideDatasetActionoutput_sam": {
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150 "action_arguments": {},
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151 "action_type": "HideDatasetAction",
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152 "output_name": "output_sam"
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153 },
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154 "HideDatasetActionoutput_unaligned_reads_l": {
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155 "action_arguments": {},
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156 "action_type": "HideDatasetAction",
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157 "output_name": "output_unaligned_reads_l"
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158 },
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159 "HideDatasetActionoutput_unaligned_reads_r": {
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160 "action_arguments": {},
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161 "action_type": "HideDatasetAction",
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162 "output_name": "output_unaligned_reads_r"
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163 }
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164 },
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165 "tool_errors": null,
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166 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2",
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167 "tool_shed_repository": {
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168 "changeset_revision": "a9d4f71dbfb0",
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169 "name": "bowtie2",
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170 "owner": "devteam",
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171 "tool_shed": "toolshed.g2.bx.psu.edu"
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172 },
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173 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\"}\", \"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\\\": {\\\"int_quals\\\": \\\"false\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}",
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174 "tool_version": "2.2.6.2",
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175 "type": "tool",
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176 "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126",
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177 "workflow_outputs": []
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178 },
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179 "3": {
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180 "annotation": "",
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181 "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2",
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182 "id": 3,
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183 "input_connections": {
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184 "input": {
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185 "id": 2,
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217 "action_type": "HideDatasetAction",
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220 },
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224 "changeset_revision": "201c568972c3",
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225 "name": "concatenate_multiple_datasets",
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226 "owner": "mvdbeek",
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228 },
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230 "tool_version": "0.2",
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234 },
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236 "annotation": "",
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240 "libraries_0|files_0|file_type|unpaired_reads": {
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242 "output_name": "out_file1"
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243 }
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244 },
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247 "name": "spades",
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248 "outputs": [
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249 {
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250 "name": "out_contigs",
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251 "type": "fasta"
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252 },
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253 {
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254 "name": "out_contig_stats",
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255 "type": "tabular"
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256 },
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257 {
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258 "name": "out_scaffolds",
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259 "type": "fasta"
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260 },
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261 {
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262 "name": "out_scaffold_stats",
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263 "type": "tabular"
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264 },
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265 {
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266 "name": "out_log",
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267 "type": "txt"
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269 ],
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270 "position": {
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271 "left": 1084.5,
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274 "post_job_actions": {
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275 "HideDatasetActionout_contig_stats": {
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276 "action_arguments": {},
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277 "action_type": "HideDatasetAction",
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278 "output_name": "out_contig_stats"
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279 },
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280 "HideDatasetActionout_contigs": {
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281 "action_arguments": {},
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308 },
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324 },
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346 "tool_shed_repository": {
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348 "name": "fasta_filter_by_length",
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349 "owner": "devteam",
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350 "tool_shed": "toolshed.g2.bx.psu.edu"
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356 "workflow_outputs": [
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357 {
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359 "output_name": "output",
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363 },
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364 "6": {
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369 "db_opts|histdb": {
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371 "output_name": "output"
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372 },
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430 "sequences": {
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432 "output_name": "output"
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437 "description": "runtime parameter for tool Parse blast output and compile hits",
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438 "name": "blast"
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441 "description": "runtime parameter for tool Parse blast output and compile hits",
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442 "name": "sequences"
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446 "name": "Parse blast output and compile hits",
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447 "outputs": [
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449 "name": "tabularOutput",
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453 "name": "fastaOutput",
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458 "type": "fasta"
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461 "name": "un_sequences",
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462 "type": "fasta"
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465 "position": {
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ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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467 "top": 203.5625
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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468 },
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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469 "post_job_actions": {
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470 "HideDatasetActional_sequences": {
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471 "action_arguments": {},
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472 "action_type": "HideDatasetAction",
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473 "output_name": "al_sequences"
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474 },
ba15c770fd40 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
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475 "HideDatasetActionfastaOutput": {
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476 "action_arguments": {},
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477 "action_type": "HideDatasetAction",
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478 "output_name": "fastaOutput"
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479 },
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480 "HideDatasetActionun_sequences": {
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481 "action_arguments": {},
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482 "action_type": "HideDatasetAction",
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483 "output_name": "un_sequences"
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484 }
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485 },
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486 "tool_errors": null,
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487 "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3",
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488 "tool_shed_repository": {
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489 "changeset_revision": "1991c830504a",
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490 "name": "msp_blastparser_and_hits",
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491 "owner": "drosofff",
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492 "tool_shed": "toolshed.g2.bx.psu.edu"
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493 },
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494 "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
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495 "tool_version": "2.4.3",
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496 "type": "tool",
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497 "uuid": "30288e33-ff64-4089-9b45-428027744176",
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498 "workflow_outputs": [
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499 {
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500 "label": null,
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501 "output_name": "tabularOutput",
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502 "uuid": "6b25acfc-474c-4852-b196-a14a4cf619e3"
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503 }
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504 ]
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505 }
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506 },
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507 "uuid": "d0251632-aef7-4c9b-9617-140c9fbab352"
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508 }