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Replace several tabular manipulations with regex_replace tool
author Jim Johnson <jj@umn.edu>
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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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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diff changeset
311 "10": {
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312 "annotation": "Add a column with the RSEM TPM times a million.",
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diff changeset
313 "id": 10,
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parents:
diff changeset
314 "input_connections": {
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parents:
diff changeset
315 "input": {
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parents:
diff changeset
316 "id": 9,
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diff changeset
317 "output_name": "out_file1"
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diff changeset
318 }
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diff changeset
319 },
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diff changeset
320 "inputs": [],
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321 "name": "Compute",
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322 "outputs": [
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323 {
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diff changeset
324 "name": "out_file1",
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325 "type": "input"
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326 }
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diff changeset
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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diff changeset
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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diff changeset
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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diff changeset
340 "11": {
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diff changeset
341 "annotation": "",
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diff changeset
342 "id": 11,
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diff changeset
343 "input_connections": {
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344 "input1": {
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345 "id": 7,
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diff changeset
346 "output_name": "outfile"
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diff changeset
347 },
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diff changeset
348 "input2": {
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349 "id": 10,
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diff changeset
350 "output_name": "out_file1"
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diff changeset
351 }
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diff changeset
352 },
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diff changeset
353 "inputs": [],
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diff changeset
354 "name": "Join two Datasets",
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diff changeset
355 "outputs": [
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diff changeset
356 {
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diff changeset
357 "name": "out_file1",
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diff changeset
358 "type": "input"
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diff changeset
359 }
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
360 ],
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361 "position": {
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diff changeset
362 "left": 1350,
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Jim Johnson <jj@umn.edu>
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363 "top": 419
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diff changeset
364 },
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diff changeset
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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diff changeset
369 "tool_version": "2.0.2",
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diff changeset
370 "type": "tool",
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diff changeset
371 "user_outputs": []
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diff changeset
372 },
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diff changeset
373 "12": {
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374 "annotation": "",
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parents:
diff changeset
375 "id": 12,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
376 "input_connections": {
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
377 "infile": {
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
378 "id": 11,
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diff changeset
379 "output_name": "out_file1"
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diff changeset
380 }
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diff changeset
381 },
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diff changeset
382 "inputs": [],
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Jim Johnson <jj@umn.edu>
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diff changeset
383 "name": "Regex Replace",
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Jim Johnson <jj@umn.edu>
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diff changeset
384 "outputs": [
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diff changeset
385 {
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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parents:
diff changeset
386 "name": "outfile",
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diff changeset
387 "type": "txt"
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parents:
diff changeset
388 }
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Jim Johnson <jj@umn.edu>
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diff changeset
389 ],
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
390 "position": {
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Jim Johnson <jj@umn.edu>
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diff changeset
391 "left": 1545,
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Jim Johnson <jj@umn.edu>
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392 "top": 546
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parents:
diff changeset
393 },
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parents:
diff changeset
394 "post_job_actions": {
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diff changeset
395 "ChangeDatatypeActionoutfile": {
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parents:
diff changeset
396 "action_arguments": {
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parents:
diff changeset
397 "newtype": "tabular"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
398 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
399 "action_type": "ChangeDatatypeAction",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
400 "output_name": "outfile"
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
401 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
402 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
403 "tool_errors": null,
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parents:
diff changeset
404 "tool_id": "toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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diff changeset
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\\\"\"}",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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parents:
diff changeset
406 "tool_version": "1.0.0",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
407 "type": "tool",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
408 "user_outputs": []
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
409 },
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diff changeset
410 "13": {
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diff changeset
411 "annotation": "Final reduced database after application of a TPM cut-off.",
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parents:
diff changeset
412 "id": 13,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
413 "input_connections": {
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
414 "input": {
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
415 "id": 12,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
416 "output_name": "outfile"
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
417 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
418 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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diff changeset
419 "inputs": [],
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
420 "name": "Tabular-to-FASTA",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
421 "outputs": [
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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diff changeset
422 {
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parents:
diff changeset
423 "name": "output",
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Jim Johnson <jj@umn.edu>
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diff changeset
424 "type": "fasta"
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parents:
diff changeset
425 }
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parents:
diff changeset
426 ],
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
427 "position": {
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Jim Johnson <jj@umn.edu>
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diff changeset
428 "left": 1743,
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Jim Johnson <jj@umn.edu>
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diff changeset
429 "top": 484
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
430 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
431 "post_job_actions": {},
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parents:
diff changeset
432 "tool_errors": null,
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parents:
diff changeset
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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diff changeset
435 "tool_version": "1.1.0",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
436 "type": "tool",
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parents:
diff changeset
437 "user_outputs": []
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parents:
diff changeset
438 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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diff changeset
439 "14": {
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diff changeset
440 "annotation": "Format FASTA to desired width.",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
441 "id": 14,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
442 "input_connections": {
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
443 "input": {
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
444 "id": 13,
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
445 "output_name": "output"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
446 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
447 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
448 "inputs": [],
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
449 "name": "FASTA Width",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
450 "outputs": [
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
451 {
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
452 "name": "output",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
453 "type": "input"
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
454 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
455 ],
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
456 "position": {
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
457 "left": 1939,
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Jim Johnson <jj@umn.edu>
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diff changeset
458 "top": 569
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
459 },
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
460 "post_job_actions": {},
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
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diff changeset
461 "tool_errors": null,
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diff changeset
462 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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parents:
diff changeset
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\\\"\"}",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
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diff changeset
464 "tool_version": "1.0.0",
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Jim Johnson <jj@umn.edu>
parents:
diff changeset
465 "type": "tool",
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
466 "user_outputs": []
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
467 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
468 }
20d9fb1ba210 Replace several tabular manipulations with regex_replace tool
Jim Johnson <jj@umn.edu>
parents:
diff changeset
469 }