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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
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4 "format-version": "0.1",
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5 "name": "Species of top BLAST hits",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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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": "",
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14 "name": "Transcriptome FASTA file"
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15 }
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16 ],
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17 "label": null,
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18 "name": "Input dataset",
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19 "outputs": [],
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20 "position": {
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21 "left": 242,
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22 "top": 119
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23 },
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24 "tool_errors": null,
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25 "tool_id": null,
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26 "tool_state": "{\"name\": \"Transcriptome FASTA file\"}",
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27 "tool_version": null,
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28 "type": "data_input",
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29 "user_outputs": [],
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30 "uuid": "e445b44b-02a7-4fd1-8944-cd680f967062"
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31 },
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32 "1": {
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33 "annotation": "This workflow is deliberately a simple/crude assessment, and there is no need to run BLASTX on all the sequences - a sample of 1000 should be enough.",
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34 "id": 1,
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35 "input_connections": {
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36 "input_file": {
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37 "id": 0,
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38 "output_name": "output"
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39 }
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40 },
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41 "inputs": [],
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42 "label": null,
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43 "name": "Sub-sample sequences files",
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44 "outputs": [
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45 {
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46 "name": "output_file",
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47 "type": "input"
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48 }
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49 ],
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50 "position": {
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51 "left": 435,
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52 "top": 119
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53 },
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54 "post_job_actions": {
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55 "RenameDatasetActionoutput_file": {
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56 "action_arguments": {
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57 "newname": "1000 sequences from #{input_file}"
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58 },
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59 "action_type": "RenameDatasetAction",
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60 "output_name": "output_file"
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61 }
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62 },
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63 "tool_errors": null,
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64 "tool_id": "toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1",
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65 "tool_state": "{\"__page__\": 0, \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"sampling\": \"{\\\"count\\\": \\\"1000\\\", \\\"type\\\": \\\"desired_count\\\", \\\"__current_case__\\\": 2}\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"interleaved\": \"\\\"False\\\"\"}",
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66 "tool_version": "0.2.1",
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67 "type": "tool",
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68 "user_outputs": [],
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69 "uuid": "87ce69ef-5fb0-41b0-9575-d3b96544f8be"
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70 },
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71 "2": {
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72 "annotation": "We only want one line per query, so limit this to the best scoring target sequence. Assumes current NCBI nr database is available locally as \"nr\".",
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73 "id": 2,
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74 "input_connections": {
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75 "query": {
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76 "id": 1,
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77 "output_name": "output_file"
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78 }
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79 },
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80 "inputs": [],
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81 "label": null,
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82 "name": "NCBI BLAST+ blastx",
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83 "outputs": [
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84 {
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85 "name": "output1",
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86 "type": "tabular"
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87 }
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88 ],
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89 "position": {
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90 "left": 489,
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91 "top": 263
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92 },
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93 "post_job_actions": {
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94 "RenameDatasetActionoutput1": {
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95 "action_arguments": {
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96 "newname": "Top BLAST match"
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97 },
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98 "action_type": "RenameDatasetAction",
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99 "output_name": "output1"
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100 }
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101 },
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102 "tool_errors": null,
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103 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.01",
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104 "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_optional_id_files_opts\\\": {\\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\", \\\"__current_case__\\\": 0}, \\\"matrix\\\": \\\"BLOSUM62\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"True\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"db\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"database\\\": \\\"nr\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"query\": \"null\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": [\\\"staxids\\\", \\\"sscinames\\\", \\\"scomnames\\\", \\\"sblastnames\\\", \\\"sskingdoms\\\"], \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": null}\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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105 "tool_version": "0.1.01",
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106 "type": "tool",
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107 "user_outputs": [],
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108 "uuid": "1559a0b0-0b66-40f9-b777-2f062fcda4cc"
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109 },
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110 "3": {
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111 "annotation": "Having a tabular file of all 1000 sequences is used in the \"join\" step to count the sequences giving no BLAST hit.",
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112 "id": 3,
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113 "input_connections": {
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114 "input": {
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115 "id": 1,
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116 "output_name": "output_file"
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117 }
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118 },
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119 "inputs": [],
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120 "label": null,
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121 "name": "FASTA-to-Tabular",
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122 "outputs": [
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123 {
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124 "name": "output",
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125 "type": "tabular"
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126 }
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127 ],
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128 "position": {
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129 "left": 696,
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130 "top": 139
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131 },
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132 "post_job_actions": {
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133 "HideDatasetActionoutput": {
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134 "action_arguments": {},
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135 "action_type": "HideDatasetAction",
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136 "output_name": "output"
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137 },
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138 "RenameDatasetActionoutput": {
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139 "action_arguments": {
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140 "newname": "1000 sequences as tabular"
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141 },
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142 "action_type": "RenameDatasetAction",
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143 "output_name": "output"
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144 }
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145 },
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146 "tool_errors": null,
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147 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0",
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148 "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"2\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
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149 "tool_version": "1.1.0",
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150 "type": "tool",
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151 "user_outputs": [],
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152 "uuid": "31f11208-b2bd-4d9d-9745-dc1a6ed7ccf9"
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153 },
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154 "4": {
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155 "annotation": "Some BLAST matches will give multiple HSPs, and thus multiple lines in the tabular output. We only want one line per query.",
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156 "id": 4,
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157 "input_connections": {
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158 "input": {
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159 "id": 2,
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160 "output_name": "output1"
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161 }
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162 },
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163 "inputs": [],
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164 "label": null,
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165 "name": "Unique",
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166 "outputs": [
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167 {
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168 "name": "outfile",
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169 "type": "input"
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170 }
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171 ],
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172 "position": {
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173 "left": 665,
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174 "top": 376
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175 },
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176 "post_job_actions": {
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177 "HideDatasetActionoutfile": {
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178 "action_arguments": {},
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179 "action_type": "HideDatasetAction",
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180 "output_name": "outfile"
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181 },
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182 "RenameDatasetActionoutfile": {
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183 "action_arguments": {
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184 "newname": "One HSP per BLAST hit"
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185 },
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186 "action_type": "RenameDatasetAction",
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187 "output_name": "outfile"
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188 }
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189 },
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190 "tool_errors": null,
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191 "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3",
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192 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"column_end\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"column_start\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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193 "tool_version": "0.3",
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194 "type": "tool",
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195 "user_outputs": [],
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196 "uuid": "acf948e3-71dc-4f35-8357-3998bd0abdd8"
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197 },
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198 "5": {
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199 "annotation": "We don't need all the columns in this join, but the key is to assign \"None\" to the sequences with no BLAST hits.",
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200 "id": 5,
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201 "input_connections": {
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202 "input1": {
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203 "id": 3,
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204 "output_name": "output"
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205 },
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206 "input2": {
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207 "id": 4,
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208 "output_name": "outfile"
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209 }
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210 },
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211 "inputs": [],
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212 "label": null,
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213 "name": "Join two Datasets",
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214 "outputs": [
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215 {
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216 "name": "out_file1",
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217 "type": "input"
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218 }
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219 ],
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220 "position": {
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221 "left": 827,
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222 "top": 263
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223 },
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224 "post_job_actions": {
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225 "HideDatasetActionout_file1": {
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226 "action_arguments": {},
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227 "action_type": "HideDatasetAction",
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228 "output_name": "out_file1"
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229 },
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230 "RenameDatasetActionout_file1": {
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231 "action_arguments": {
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232 "newname": "Top BLAST hits or None"
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233 },
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234 "action_type": "RenameDatasetAction",
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235 "output_name": "out_file1"
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236 }
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237 },
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238 "tool_errors": null,
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239 "tool_id": "join1",
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240 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"fill_empty\\\", \\\"do_fill_empty_columns\\\": {\\\"column_fill_type\\\": \\\"single_fill_value\\\", \\\"fill_value\\\": \\\"None\\\", \\\"__current_case__\\\": 0}, \\\"fill_columns_by\\\": \\\"fill_unjoined_only\\\", \\\"__current_case__\\\": 1}\", \"unmatched\": \"\\\"-u\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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241 "tool_version": "2.0.2",
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242 "type": "tool",
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243 "user_outputs": [],
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244 "uuid": "4c280b0e-b4a6-4ae4-8a81-d6e93932ef71"
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245 },
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246 "6": {
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247 "annotation": "Here we make a tally table of the BLAST species name column",
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248 "id": 6,
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249 "input_connections": {
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250 "input": {
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251 "id": 5,
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252 "output_name": "out_file1"
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253 }
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254 },
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255 "inputs": [],
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256 "label": null,
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257 "name": "Count",
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258 "outputs": [
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259 {
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260 "name": "out_file1",
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261 "type": "tabular"
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262 }
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263 ],
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264 "position": {
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265 "left": 952,
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266 "top": 398
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267 },
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268 "post_job_actions": {
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271 "action_type": "HideDatasetAction",
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272 "output_name": "out_file1"
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273 },
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274 "RenameDatasetActionout_file1": {
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275 "action_arguments": {
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276 "newname": "Top BLAST hit species counts (unsorted)"
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277 },
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278 "action_type": "RenameDatasetAction",
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279 "output_name": "out_file1"
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280 }
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281 },
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282 "tool_errors": null,
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283 "tool_id": "Count1",
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284 "tool_state": "{\"__page__\": 0, \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"19\\\"]}\", \"__rerun_remap_job_id__\": null, \"delim\": \"\\\"T\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
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285 "tool_version": "1.0.0",
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286 "type": "tool",
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287 "user_outputs": [],
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288 "uuid": "d3322137-1911-426d-87a7-c82b5fc16825"
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289 },
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290 "7": {
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291 "annotation": "Sorting the counts makes the results easier to interpret directly.",
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292 "id": 7,
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293 "input_connections": {
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294 "input": {
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295 "id": 6,
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296 "output_name": "out_file1"
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297 }
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298 },
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299 "inputs": [],
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300 "label": null,
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301 "name": "Sort",
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302 "outputs": [
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303 {
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304 "name": "out_file1",
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305 "type": "input"
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306 }
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307 ],
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308 "position": {
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310 "top": 506
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311 },
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312 "post_job_actions": {
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313 "RenameDatasetActionout_file1": {
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314 "action_arguments": {
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315 "newname": "Top BLAST hit species counts"
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316 },
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317 "action_type": "RenameDatasetAction",
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318 "output_name": "out_file1"
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319 }
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320 },
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321 "tool_errors": null,
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322 "tool_id": "sort1",
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323 "tool_state": "{\"__page__\": 0, \"style\": \"\\\"num\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"null\", \"chromInfo\": \"\\\"/mnt/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"order\": \"\\\"DESC\\\"\"}",
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324 "tool_version": "1.0.3",
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325 "type": "tool",
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326 "user_outputs": [],
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327 "uuid": "c81cc61d-52a3-44ee-b646-b23e0e004c38"
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328 }
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329 },
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330 "uuid": "9fe8754a-3a87-4f6a-89a2-141b02b4793e"
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331 } |
