Mercurial > repos > galaxyp > proteomics_rnaseq_reduced_db_workflow
annotate proteomics_rnaseq_reduced_db_workflow_v2.ga @ 1:20d9fb1ba210 default tip
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author | Jim Johnson <jj@umn.edu> |
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date | Thu, 20 Mar 2014 21:50:05 -0500 |
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1 { |
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2 "a_galaxy_workflow": "true", |
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3 "annotation": "Filter out proteins that have a transcript expression level, as quantified by RNA-Seq data, below a certain threshold.", |
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4 "format-version": "0.1", |
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5 "name": "Proteomics Reduced DB v2", |
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6 "steps": { |
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7 "0": { |
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8 "annotation": "ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz", |
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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": "ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/pep/Homo_sapiens.GRCh37.73.pep.all.fa.gz", |
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14 "name": "Ensembl Protein FASTA (reference proteome)" |
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15 } |
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16 ], |
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17 "name": "Input dataset", |
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18 "outputs": [], |
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19 "position": { |
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20 "left": 208, |
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21 "top": 200 |
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22 }, |
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23 "tool_errors": null, |
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24 "tool_id": null, |
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25 "tool_state": "{\"name\": \"Ensembl Protein FASTA (reference proteome)\"}", |
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26 "tool_version": null, |
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27 "type": "data_input", |
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28 "user_outputs": [] |
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29 }, |
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30 "1": { |
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31 "annotation": "Ensembl reference fasta with only chromosome assigned sequences. For example: ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.toplevel.fa.gz", |
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32 "id": 1, |
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33 "input_connections": {}, |
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34 "inputs": [ |
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35 { |
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36 "description": "Ensembl reference fasta with only chromosome assigned sequences. For example: ftp://ftp.ensembl.org/pub/release-73/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.73.dna.toplevel.fa.gz", |
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37 "name": "Ensembl Genome Reference Fasta" |
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38 } |
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39 ], |
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40 "name": "Input dataset", |
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41 "outputs": [], |
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42 "position": { |
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43 "left": 209, |
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44 "top": 292 |
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45 }, |
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46 "tool_errors": null, |
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47 "tool_id": null, |
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48 "tool_state": "{\"name\": \"Ensembl Genome Reference Fasta\"}", |
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49 "tool_version": null, |
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50 "type": "data_input", |
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51 "user_outputs": [] |
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52 }, |
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53 "2": { |
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54 "annotation": "For example: \nftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz", |
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55 "id": 2, |
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56 "input_connections": {}, |
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57 "inputs": [ |
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58 { |
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59 "description": "For example: \nftp://ftp.ensembl.org/pub/release-73/gtf/homo_sapiens/Homo_sapiens.GRCh37.73.gtf.gz", |
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60 "name": "Ensembl GTF File (gene models)" |
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61 } |
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62 ], |
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63 "name": "Input dataset", |
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64 "outputs": [], |
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65 "position": { |
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66 "left": 213, |
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67 "top": 456 |
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68 }, |
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69 "tool_errors": null, |
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70 "tool_id": null, |
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71 "tool_state": "{\"name\": \"Ensembl GTF File (gene models)\"}", |
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72 "tool_version": null, |
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73 "type": "data_input", |
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74 "user_outputs": [] |
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75 }, |
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76 "3": { |
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77 "annotation": "RNA-Seq left mate pair fastq (These should be in fastqsanger format. If not, convert with \"Fastq Groomer\" tool.)", |
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78 "id": 3, |
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79 "input_connections": {}, |
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80 "inputs": [ |
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81 { |
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82 "description": "RNA-Seq left mate pair fastq (These should be in fastqsanger format. If not, convert with \"Fastq Groomer\" tool.)", |
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83 "name": "RNA-Seq left paired-end fastq" |
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84 } |
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85 ], |
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86 "name": "Input dataset", |
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87 "outputs": [], |
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88 "position": { |
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89 "left": 220, |
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90 "top": 563 |
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91 }, |
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92 "tool_errors": null, |
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93 "tool_id": null, |
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94 "tool_state": "{\"name\": \"RNA-Seq left paired-end fastq\"}", |
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95 "tool_version": null, |
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96 "type": "data_input", |
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97 "user_outputs": [] |
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98 }, |
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99 "4": { |
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100 "annotation": "RNA-Seq right mate pair fastq (These should be in fastqsanger format. If not, convert with \"Fastq Groomer\" tool.)", |
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101 "id": 4, |
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102 "input_connections": {}, |
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103 "inputs": [ |
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104 { |
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105 "description": "RNA-Seq right mate pair fastq (These should be in fastqsanger format. If not, convert with \"Fastq Groomer\" tool.)", |
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106 "name": "RNA-Seq right paired-end fastq" |
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107 } |
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108 ], |
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109 "name": "Input dataset", |
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110 "outputs": [], |
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111 "position": { |
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112 "left": 221, |
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113 "top": 673 |
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114 }, |
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115 "tool_errors": null, |
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116 "tool_id": null, |
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117 "tool_state": "{\"name\": \"RNA-Seq right paired-end fastq\"}", |
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118 "tool_version": null, |
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119 "type": "data_input", |
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120 "user_outputs": [] |
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121 }, |
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122 "5": { |
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123 "annotation": "Convert peptide fasta to a 2-column tabular file. Keep all the head info.", |
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124 "id": 5, |
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125 "input_connections": { |
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126 "input": { |
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127 "id": 0, |
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128 "output_name": "output" |
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129 } |
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130 }, |
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131 "inputs": [], |
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132 "name": "FASTA-to-Tabular", |
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133 "outputs": [ |
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134 { |
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135 "name": "output", |
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136 "type": "tabular" |
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137 } |
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138 ], |
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139 "position": { |
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140 "left": 538, |
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141 "top": 267 |
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142 }, |
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143 "post_job_actions": {}, |
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144 "tool_errors": null, |
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145 "tool_id": "fasta2tab", |
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146 "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"__rerun_remap_job_id__\": null}", |
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147 "tool_version": "1.1.0", |
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148 "type": "tool", |
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149 "user_outputs": [] |
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150 }, |
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151 "6": { |
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152 "annotation": "Given a GTF file and the reference genome, this tool constructs a synthetic transcriptome that will be used for isoform quantification during \"-calculate expression\".", |
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153 "id": 6, |
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154 "input_connections": { |
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155 "reference|gtf": { |
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156 "id": 2, |
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157 "output_name": "output" |
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158 }, |
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159 "reference|reference_fasta_file": { |
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160 "id": 1, |
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161 "output_name": "output" |
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162 } |
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163 }, |
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164 "inputs": [], |
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165 "name": "RSEM prepare reference", |
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166 "outputs": [ |
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167 { |
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168 "name": "reference_file", |
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169 "type": "rsem_ref" |
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170 } |
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171 ], |
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172 "position": { |
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173 "left": 419, |
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174 "top": 388 |
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175 }, |
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176 "post_job_actions": {}, |
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177 "tool_errors": null, |
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178 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17", |
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179 "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"ref_type\\\": \\\"genomic\\\", \\\"gtf\\\": null, \\\"reference_fasta_file\\\": null, \\\"__current_case__\\\": 1}\", \"reference_name\": \"\\\"primaryEnsemblGtfRef\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"polya\": \"{\\\"polya_use\\\": \\\"add\\\", \\\"polya_length\\\": \\\"125\\\", \\\"__current_case__\\\": 0}\", \"transcript_to_gene_map\": \"null\", \"ntog\": \"\\\"False\\\"\"}", |
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180 "tool_version": "1.1.17", |
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181 "type": "tool", |
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182 "user_outputs": [] |
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183 }, |
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184 "7": { |
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185 "annotation": "", |
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186 "id": 7, |
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187 "input_connections": { |
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188 "infile": { |
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189 "id": 5, |
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190 "output_name": "output" |
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191 } |
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192 }, |
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193 "inputs": [], |
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194 "name": "Regex Replace", |
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195 "outputs": [ |
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196 { |
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197 "name": "outfile", |
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198 "type": "txt" |
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199 } |
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200 ], |
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201 "position": { |
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202 "left": 802, |
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203 "top": 281 |
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204 }, |
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205 "post_job_actions": { |
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206 "ChangeDatatypeActionoutfile": { |
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207 "action_arguments": { |
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208 "newtype": "tabular" |
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209 }, |
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210 "action_type": "ChangeDatatypeAction", |
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211 "output_name": "outfile" |
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212 } |
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213 }, |
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214 "tool_errors": null, |
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215 "tool_id": "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0", |
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216 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"search_str\": \"\\\"^(.* transcript:)(ENST\\\\\\\\d+)(.*)$\\\"\", \"__rerun_remap_job_id__\": null, \"replace_str\": \"\\\"\\\\\\\\1\\\\\\\\2\\\\\\\\3\\\\\\\\t\\\\\\\\2\\\"\", \"replace_count\": \"\\\"0\\\"\", \"multiline\": \"\\\"False\\\"\", \"infile\": \"null\", \"dot_all\": \"\\\"False\\\"\"}", |
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217 "tool_version": "1.0.0", |
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218 "type": "tool", |
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219 "user_outputs": [] |
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220 }, |
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221 "8": { |
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222 "annotation": "Given then RNA-Seq reads (fastq) and synthetic transcriptome (from \"-prepare reference\"), this tool quantifies the abundances of each mRNA transcript within the GTF file.", |
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223 "id": 8, |
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224 "input_connections": { |
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225 "input|fastq|fastq1": { |
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226 "id": 3, |
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227 "output_name": "output" |
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228 }, |
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229 "input|fastq|fastq2": { |
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230 "id": 4, |
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231 "output_name": "output" |
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232 }, |
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233 "reference|rsem_ref": { |
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234 "id": 6, |
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235 "output_name": "reference_file" |
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236 } |
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237 }, |
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238 "inputs": [], |
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239 "name": "RSEM calculate expression", |
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240 "outputs": [ |
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241 { |
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242 "name": "gene_abundances", |
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243 "type": "tabular" |
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244 }, |
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245 { |
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246 "name": "isoform_abundances", |
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247 "type": "tabular" |
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248 }, |
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249 { |
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250 "name": "transcript_bam", |
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251 "type": "bam" |
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252 }, |
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253 { |
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254 "name": "transcript_sorted_bam", |
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255 "type": "bam" |
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256 }, |
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257 { |
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258 "name": "genome_bam", |
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259 "type": "bam" |
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260 }, |
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261 { |
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262 "name": "genome_sorted_bam", |
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263 "type": "bam" |
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264 }, |
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265 { |
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266 "name": "log", |
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267 "type": "txt" |
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268 } |
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269 ], |
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270 "position": { |
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271 "left": 719, |
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272 "top": 523 |
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273 }, |
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274 "post_job_actions": {}, |
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275 "tool_errors": null, |
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276 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17", |
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277 "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"rsem_ref\\\": null, \\\"refSrc\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\", \"rsem_options\": \"{\\\"fullparams\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"rsem_outputs\": \"{\\\"result_bams\\\": \\\"none\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"seedlength\": \"\\\"25\\\"\", \"sample\": \"\\\"rsem_sample\\\"\", \"forward_prob\": \"\\\"0.5\\\"\", \"input\": \"{\\\"fastq\\\": {\\\"fastq2\\\": null, \\\"fastq1\\\": null, \\\"matepair\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}, \\\"bowtie_options\\\": {\\\"fullparams\\\": \\\"default\\\", \\\"__current_case__\\\": 0}, \\\"fastq_select\\\": \\\"--phred33-quals\\\", \\\"__current_case__\\\": 0, \\\"format\\\": \\\"fastq\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", |
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278 "tool_version": "1.1.17", |
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279 "type": "tool", |
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280 "user_outputs": [] |
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281 }, |
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282 "9": { |
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283 "annotation": "Selection of lower threshold of transcriptional abundance in TPM required for inclusion of the corresponding protein in the reduced database.", |
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284 "id": 9, |
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285 "input_connections": { |
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286 "input": { |
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287 "id": 8, |
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288 "output_name": "isoform_abundances" |
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289 } |
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290 }, |
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291 "inputs": [], |
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292 "name": "Filter", |
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293 "outputs": [ |
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294 { |
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295 "name": "out_file1", |
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296 "type": "input" |
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297 } |
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298 ], |
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299 "position": { |
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300 "left": 991, |
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301 "top": 591 |
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302 }, |
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303 "post_job_actions": {}, |
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304 "tool_errors": null, |
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305 "tool_id": "Filter1", |
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306 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c3>0.000001\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", |
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307 "tool_version": "1.1.0", |
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308 "type": "tool", |
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309 "user_outputs": [] |
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310 }, |
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311 "10": { |
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312 "annotation": "Add a column with the RSEM TPM times a million.", |
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313 "id": 10, |
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314 "input_connections": { |
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315 "input": { |
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316 "id": 9, |
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317 "output_name": "out_file1" |
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318 } |
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319 }, |
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320 "inputs": [], |
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321 "name": "Compute", |
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322 "outputs": [ |
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323 { |
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324 "name": "out_file1", |
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325 "type": "input" |
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326 } |
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327 ], |
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328 "position": { |
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329 "left": 1199, |
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330 "top": 574 |
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331 }, |
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332 "post_job_actions": {}, |
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333 "tool_errors": null, |
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334 "tool_id": "Add_a_column1", |
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335 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c3*1000000\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"round\": \"\\\"no\\\"\"}", |
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336 "tool_version": "1.1.0", |
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337 "type": "tool", |
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338 "user_outputs": [] |
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339 }, |
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340 "11": { |
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341 "annotation": "", |
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342 "id": 11, |
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343 "input_connections": { |
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344 "input1": { |
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345 "id": 7, |
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346 "output_name": "outfile" |
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347 }, |
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348 "input2": { |
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349 "id": 10, |
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350 "output_name": "out_file1" |
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351 } |
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352 }, |
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353 "inputs": [], |
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354 "name": "Join two Datasets", |
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355 "outputs": [ |
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356 { |
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357 "name": "out_file1", |
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358 "type": "input" |
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359 } |
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360 ], |
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361 "position": { |
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362 "left": 1350, |
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363 "top": 419 |
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364 }, |
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365 "post_job_actions": {}, |
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366 "tool_errors": null, |
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367 "tool_id": "join1", |
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368 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"field1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"partial\": \"\\\"\\\"\", \"field2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"fill_empty_columns\": \"{\\\"fill_empty_columns_switch\\\": \\\"no_fill\\\", \\\"__current_case__\\\": 0}\", \"unmatched\": \"\\\"\\\"\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", |
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369 "tool_version": "2.0.2", |
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370 "type": "tool", |
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371 "user_outputs": [] |
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372 }, |
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373 "12": { |
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374 "annotation": "", |
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375 "id": 12, |
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376 "input_connections": { |
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377 "infile": { |
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378 "id": 11, |
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379 "output_name": "out_file1" |
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380 } |
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381 }, |
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382 "inputs": [], |
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383 "name": "Regex Replace", |
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384 "outputs": [ |
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385 { |
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386 "name": "outfile", |
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387 "type": "txt" |
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388 } |
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389 ], |
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390 "position": { |
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391 "left": 1545, |
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392 "top": 546 |
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393 }, |
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394 "post_job_actions": { |
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395 "ChangeDatatypeActionoutfile": { |
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396 "action_arguments": { |
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397 "newtype": "tabular" |
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398 }, |
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399 "action_type": "ChangeDatatypeAction", |
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400 "output_name": "outfile" |
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401 } |
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402 }, |
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403 "tool_errors": null, |
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404 "tool_id": "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0", |
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405 "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"search_str\": \"\\\"^(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)\\\\\\\\t(.*)$\\\"\", \"__rerun_remap_job_id__\": null, \"replace_str\": \"\\\"\\\\\\\\1 tmp:\\\\\\\\8\\\\\\\\t\\\\\\\\2\\\"\", \"replace_count\": \"\\\"0\\\"\", \"multiline\": \"\\\"False\\\"\", \"infile\": \"null\", \"dot_all\": \"\\\"False\\\"\"}", |
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406 "tool_version": "1.0.0", |
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407 "type": "tool", |
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408 "user_outputs": [] |
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409 }, |
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410 "13": { |
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411 "annotation": "Final reduced database after application of a TPM cut-off.", |
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412 "id": 13, |
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413 "input_connections": { |
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414 "input": { |
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415 "id": 12, |
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416 "output_name": "outfile" |
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417 } |
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418 }, |
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419 "inputs": [], |
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420 "name": "Tabular-to-FASTA", |
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421 "outputs": [ |
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422 { |
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423 "name": "output", |
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424 "type": "fasta" |
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425 } |
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426 ], |
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427 "position": { |
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428 "left": 1743, |
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429 "top": 484 |
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430 }, |
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431 "post_job_actions": {}, |
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432 "tool_errors": null, |
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433 "tool_id": "tab2fasta", |
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434 "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\"}", |
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435 "tool_version": "1.1.0", |
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436 "type": "tool", |
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437 "user_outputs": [] |
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438 }, |
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439 "14": { |
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440 "annotation": "Format FASTA to desired width.", |
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441 "id": 14, |
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442 "input_connections": { |
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443 "input": { |
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444 "id": 13, |
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445 "output_name": "output" |
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446 } |
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447 }, |
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448 "inputs": [], |
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449 "name": "FASTA Width", |
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450 "outputs": [ |
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451 { |
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452 "name": "output", |
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453 "type": "input" |
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454 } |
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455 ], |
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456 "position": { |
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457 "left": 1939, |
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458 "top": 569 |
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459 }, |
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460 "post_job_actions": {}, |
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461 "tool_errors": null, |
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462 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0", |
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463 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/GRCm38_canon.len\\\"\", \"width\": \"\\\"80\\\"\"}", |
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464 "tool_version": "1.0.0", |
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465 "type": "tool", |
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466 "user_outputs": [] |
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467 } |
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468 } |
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469 } |