annotate Proteomics_Splice_DB_from_Paired_End_RNAseq_cached_ref.ga @ 0:3e7ebf62c90f draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author galaxyp
date Tue, 10 May 2016 18:12:00 -0400
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3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Create a peptide fasta database with novel splice junctions that are inferred from Paired End \nRNAseq data",
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5 "name": "Proteomics Splice DB from Paired End RNAseq cached ref",
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6 "steps": {
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7 "0": {
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15 "name": "RNA-Seq left mate pair fastq"
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16 }
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17 ],
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19 "name": "Input dataset",
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20 "outputs": [],
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24 },
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27 "tool_state": "{\"name\": \"RNA-Seq left mate pair fastq\"}",
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29 "type": "data_input",
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31 "workflow_outputs": [
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47 "name": "RNA-Seq right mate pair fastq"
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48 }
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49 ],
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51 "name": "Input dataset",
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52 "outputs": [],
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56 },
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59 "tool_state": "{\"name\": \"RNA-Seq right mate pair fastq\"}",
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61 "type": "data_input",
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63 "workflow_outputs": [
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64 {
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66 "output_name": "output",
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70 },
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72 "annotation": "",
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75 "input_connections": {},
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76 "inputs": [
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79 "name": "Reference genome GTF"
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80 }
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81 ],
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82 "label": null,
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83 "name": "Input dataset",
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84 "outputs": [],
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85 "position": {
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88 },
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89 "tool_errors": null,
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90 "tool_id": null,
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91 "tool_state": "{\"name\": \"Reference genome GTF\"}",
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92 "tool_version": null,
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93 "type": "data_input",
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94 "uuid": "80c391df-89f8-4846-97f1-ecad1ce5abaa",
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95 "workflow_outputs": [
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96 {
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97 "label": null,
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98 "output_name": "output",
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99 "uuid": "ed6e53c9-4937-4ada-a2af-e6d86267fe43"
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100 }
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101 ]
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102 },
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103 "3": {
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104 "annotation": "Allow novel junctions, not from the GTF\n\nBe sure to select the correct Genome Reference",
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105 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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106 "id": 3,
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107 "input_connections": {
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108 "input1": {
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109 "id": 0,
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110 "output_name": "output"
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111 },
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112 "singlePaired|input2": {
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113 "id": 1,
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114 "output_name": "output"
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115 },
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116 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
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117 "id": 2,
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118 "output_name": "output"
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119 }
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120 },
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121 "inputs": [
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122 {
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123 "description": "runtime parameter for tool TopHat for Illumina",
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124 "name": "refGenomeSource"
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125 }
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126 ],
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127 "label": null,
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128 "name": "TopHat for Illumina",
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129 "outputs": [
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130 {
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131 "name": "insertions",
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132 "type": "bed"
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133 },
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134 {
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135 "name": "deletions",
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136 "type": "bed"
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137 },
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138 {
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139 "name": "junctions",
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140 "type": "bed"
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141 },
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142 {
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143 "name": "accepted_hits",
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144 "type": "bam"
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145 }
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146 ],
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147 "position": {
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148 "left": 726,
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149 "top": 259
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150 },
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151 "post_job_actions": {},
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152 "tool_errors": null,
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153 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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154 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"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\\\": \\\"20\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"5\\\", \\\"mate_std_dev\\\": \\\"20\\\", \\\"own_junctions\\\": {\\\"gene_model_ann\\\": {\\\"gene_annotation_model\\\": null, \\\"use_annotations\\\": \\\"Yes\\\", \\\"__current_case__\\\": 1}, \\\"no_novel_juncs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"use_junctions\\\": \\\"Yes\\\", \\\"__current_case__\\\": 0, \\\"raw_juncs\\\": {\\\"use_juncs\\\": \\\"No\\\", \\\"__current_case__\\\": 0}}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"150\\\"}\"}",
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155 "tool_version": "1.5.0",
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156 "type": "tool",
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157 "uuid": "None",
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158 "workflow_outputs": [
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159 {
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160 "label": null,
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161 "output_name": "deletions",
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162 "uuid": "1eb9eafa-90f7-4717-a196-4704592381e0"
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163 },
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164 {
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165 "label": null,
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166 "output_name": "insertions",
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167 "uuid": "92733c89-05ea-4815-96ba-7ab1d3f753d2"
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168 },
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169 {
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170 "label": null,
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171 "output_name": "accepted_hits",
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172 "uuid": "22eeb200-0a5b-4580-8572-777913cda04a"
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173 },
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174 {
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175 "label": null,
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176 "output_name": "junctions",
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177 "uuid": "89706986-f95d-423a-b0ad-c616aa8e924e"
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178 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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179 ]
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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180 },
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181 "4": {
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182 "annotation": "Only look for supplied junctions\n\nBe sure to select the correct Genome Reference",
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183 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0",
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184 "id": 4,
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185 "input_connections": {
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186 "input1": {
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187 "id": 0,
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188 "output_name": "output"
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189 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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190 "singlePaired|input2": {
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191 "id": 1,
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192 "output_name": "output"
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193 },
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194 "singlePaired|pParams|own_junctions|gene_model_ann|gene_annotation_model": {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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195 "id": 2,
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196 "output_name": "output"
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197 }
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198 },
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galaxyp
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199 "inputs": [
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galaxyp
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200 {
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galaxyp
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201 "description": "runtime parameter for tool TopHat for Illumina",
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202 "name": "refGenomeSource"
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203 }
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204 ],
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205 "label": null,
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206 "name": "TopHat for Illumina",
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207 "outputs": [
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208 {
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209 "name": "insertions",
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210 "type": "bed"
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211 },
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212 {
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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213 "name": "deletions",
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214 "type": "bed"
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215 },
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216 {
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217 "name": "junctions",
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218 "type": "bed"
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219 },
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220 {
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221 "name": "accepted_hits",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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222 "type": "bam"
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223 }
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224 ],
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225 "position": {
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226 "left": 721,
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227 "top": 658
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228 },
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229 "post_job_actions": {},
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234 "type": "tool",
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235 "uuid": "None",
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236 "workflow_outputs": [
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237 {
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238 "label": null,
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239 "output_name": "deletions",
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241 },
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242 {
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243 "label": null,
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244 "output_name": "insertions",
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246 },
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247 {
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248 "label": null,
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249 "output_name": "accepted_hits",
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250 "uuid": "2fd2c931-de38-4950-b6db-dfe1c8407a00"
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251 },
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252 {
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253 "label": null,
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254 "output_name": "junctions",
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255 "uuid": "e2d804b6-7bab-4746-92eb-58db4bcfed3f"
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256 }
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257 ]
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258 },
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259 "5": {
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260 "annotation": "",
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261 "content_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
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262 "id": 5,
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263 "input_connections": {
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264 "guided_junctions": {
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265 "id": 4,
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266 "output_name": "junctions"
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267 },
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268 "input_bed": {
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269 "id": 3,
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270 "output_name": "junctions"
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271 }
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272 },
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273 "inputs": [],
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274 "label": null,
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275 "name": "Filter BED on splice junctions",
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276 "outputs": [
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277 {
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278 "name": "novel_junctions",
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279 "type": "bed"
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280 }
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281 ],
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282 "position": {
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283 "left": 1014,
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284 "top": 415
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285 },
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286 "post_job_actions": {
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287 "HideDatasetActionnovel_junctions": {
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288 "action_arguments": {},
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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diff changeset
289 "action_type": "HideDatasetAction",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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290 "output_name": "novel_junctions"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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291 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
galaxyp
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292 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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293 "tool_errors": null,
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294 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1",
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295 "tool_state": "{\"__page__\": 0, \"input_bed\": \"null\", \"__rerun_remap_job_id__\": null, \"leading_bp\": \"\\\"66\\\"\", \"guided_junctions\": \"null\", \"trailing_bp\": \"\\\"66\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCh37_canon.len\\\"\"}",
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296 "tool_version": "0.0.1",
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297 "type": "tool",
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298 "uuid": "None",
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galaxyp
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299 "workflow_outputs": []
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300 },
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301 "6": {
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302 "annotation": "",
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303 "content_id": "Extract genomic DNA 1",
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304 "id": 6,
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305 "input_connections": {
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306 "input": {
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307 "id": 5,
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308 "output_name": "novel_junctions"
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309 }
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310 },
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311 "inputs": [],
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312 "label": null,
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313 "name": "Extract Genomic DNA",
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314 "outputs": [
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315 {
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316 "name": "out_file1",
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317 "type": "input"
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318 }
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319 ],
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320 "position": {
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321 "left": 1213,
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322 "top": 621
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323 },
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324 "post_job_actions": {
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325 "HideDatasetActionout_file1": {
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326 "action_arguments": {},
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327 "action_type": "HideDatasetAction",
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328 "output_name": "out_file1"
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329 }
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330 },
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331 "tool_errors": null,
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332 "tool_id": "Extract genomic DNA 1",
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333 "tool_state": "{\"out_format\": \"\\\"interval\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"no\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}",
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334 "tool_version": "2.2.3",
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335 "type": "tool",
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336 "uuid": "None",
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337 "workflow_outputs": []
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338 },
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339 "7": {
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340 "annotation": "Set the ID prefix for generated IDs \nwhen you intend to merge multiple samples from multiple fastq inputs",
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341 "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
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342 "id": 7,
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343 "input_connections": {
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344 "input": {
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345 "id": 6,
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346 "output_name": "out_file1"
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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347 }
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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348 },
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349 "inputs": [
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350 {
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351 "description": "runtime parameter for tool Translate BED Sequences",
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352 "name": "min_length"
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353 },
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354 {
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355 "description": "runtime parameter for tool Translate BED Sequences",
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356 "name": "filter"
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357 },
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358 {
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359 "description": "runtime parameter for tool Translate BED Sequences",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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360 "name": "filter"
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361 }
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362 ],
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363 "label": null,
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364 "name": "Translate BED Sequences",
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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365 "outputs": [
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366 {
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367 "name": "translated_bed",
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368 "type": "bed"
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369 },
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370 {
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371 "name": "output",
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372 "type": "fasta"
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373 }
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374 ],
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375 "position": {
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376 "left": 1431.5,
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377 "top": 451.5
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378 },
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379 "post_job_actions": {},
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380 "tool_errors": null,
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381 "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed_sequences/translate_bed_sequences/0.1.0",
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382 "tool_state": "{\"trim\": \"{\\\"trimseqs\\\": \\\"yes\\\", \\\"__current_case__\\\": 1}\", \"min_length\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fa_sep\": \"\\\"\\\"\", \"fa_db\": \"\\\"generic\\\"\", \"reference\": \"\\\"\\\"\", \"__page__\": 0, \"refsource\": \"\\\"Ensembl\\\"\", \"__rerun_remap_job_id__\": null, \"filter\": \"{\\\"filterseqs\\\": \\\"yes\\\", \\\"trailing_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"leading_bp\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"score_name\": \"\\\"depth\\\"\", \"id_prefix\": \"\\\"\\\"\", \"input\": \"null\", \"seqtype\": \"\\\"pep:splice\\\"\"}",
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383 "tool_version": "0.1.0",
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384 "type": "tool",
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385 "uuid": "f6a04b0d-c01d-4b80-b66b-0a9e540b7cde",
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386 "workflow_outputs": [
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387 {
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388 "label": null,
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389 "output_name": "translated_bed",
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390 "uuid": "f3c4f84f-3ce8-49cc-b932-f0122d1e6f2f"
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391 },
3e7ebf62c90f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/workflows/proteogenomics_splice_junc_search_db commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
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392 {
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393 "label": "protein fasta",
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394 "output_name": "output",
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395 "uuid": "b771a5d3-fc36-4006-a967-3de09d08f3fb"
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396 }
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397 ]
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398 }
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399 },
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400 "uuid": "7799d59b-149b-457c-a248-0ae65c1b8f63"
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401 }