annotate Galaxy-Workflow-CAPS_Marker_Design_from_VCF.ga @ 4:be070a68521e draft

Uploaded workflow from vcf file to CAPS
author john-mccallum
date Thu, 18 Oct 2012 19:47:07 -0400
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be070a68521e Uploaded workflow from vcf file to CAPS
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1 {
be070a68521e Uploaded workflow from vcf file to CAPS
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2 "a_galaxy_workflow": "true",
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3 "annotation": "",
be070a68521e Uploaded workflow from vcf file to CAPS
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4 "format-version": "0.1",
be070a68521e Uploaded workflow from vcf file to CAPS
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5 "name": "CAPS Marker Design from VCF",
be070a68521e Uploaded workflow from vcf file to CAPS
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6 "steps": {
be070a68521e Uploaded workflow from vcf file to CAPS
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7 "0": {
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8 "annotation": "",
be070a68521e Uploaded workflow from vcf file to CAPS
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9 "id": 0,
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10 "input_connections": {},
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11 "inputs": [
be070a68521e Uploaded workflow from vcf file to CAPS
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12 {
be070a68521e Uploaded workflow from vcf file to CAPS
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13 "description": "",
be070a68521e Uploaded workflow from vcf file to CAPS
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14 "name": "Input Multi fasta Dataset"
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15 }
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16 ],
be070a68521e Uploaded workflow from vcf file to CAPS
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17 "name": "Input dataset",
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18 "outputs": [],
be070a68521e Uploaded workflow from vcf file to CAPS
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19 "position": {
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20 "left": 214,
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21 "top": 225
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22 },
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23 "tool_errors": null,
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24 "tool_id": null,
be070a68521e Uploaded workflow from vcf file to CAPS
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25 "tool_state": "{\"name\": \"Input Multi fasta Dataset\"}",
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26 "tool_version": null,
be070a68521e Uploaded workflow from vcf file to CAPS
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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": "",
be070a68521e Uploaded workflow from vcf file to CAPS
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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": "",
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37 "name": "Input VCF Dataset"
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38 }
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39 ],
be070a68521e Uploaded workflow from vcf file to CAPS
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40 "name": "Input dataset",
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41 "outputs": [],
be070a68521e Uploaded workflow from vcf file to CAPS
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42 "position": {
be070a68521e Uploaded workflow from vcf file to CAPS
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43 "left": 174,
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44 "top": 592
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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\": \"Input VCF Dataset\"}",
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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": "",
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55 "id": 2,
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56 "input_connections": {
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57 "inputVcf": {
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58 "id": 1,
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59 "output_name": "output"
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60 }
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61 },
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62 "inputs": [],
be070a68521e Uploaded workflow from vcf file to CAPS
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63 "name": "Convert vcf to gff",
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64 "outputs": [
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65 {
be070a68521e Uploaded workflow from vcf file to CAPS
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66 "name": "outputfile",
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67 "type": "gff3"
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68 }
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69 ],
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70 "position": {
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71 "left": 460.99998474121094,
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72 "top": 568
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73 },
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74 "post_job_actions": {},
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75 "tool_errors": null,
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76 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/vcf2gff_1/1.0.0",
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77 "tool_state": "{\"inputVcf\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
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78 "tool_version": "1.0.0",
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79 "type": "tool",
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80 "user_outputs": []
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81 },
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82 "3": {
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83 "annotation": "Detect resitriction polymorphisms",
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84 "id": 3,
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85 "input_connections": {
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86 "inputFasta": {
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87 "id": 0,
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88 "output_name": "output"
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89 },
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90 "inputSNPGff3File": {
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91 "id": 2,
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92 "output_name": "outputfile"
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93 }
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94 },
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95 "inputs": [],
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96 "name": "CAPS Detection",
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97 "outputs": [
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98 {
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99 "name": "outputfile",
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100 "type": "interval"
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101 }
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102 ],
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103 "position": {
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104 "left": 646.99998474121094,
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105 "top": 382
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106 },
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107 "post_job_actions": {},
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108 "tool_errors": null,
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109 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/CAPS_Marker_Design_2/1.0.0",
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110 "tool_state": "{\"inputFasta\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputSNPGff3File\": \"null\", \"__page__\": 0}",
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111 "tool_version": "1.0.0",
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112 "type": "tool",
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113 "user_outputs": []
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114 },
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115 "4": {
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116 "annotation": "get feature ID column",
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117 "id": 4,
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118 "input_connections": {
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119 "input": {
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120 "id": 3,
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121 "output_name": "outputfile"
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122 }
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123 },
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124 "inputs": [],
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125 "name": "Cut",
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126 "outputs": [
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127 {
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128 "name": "out_file1",
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129 "type": "tabular"
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130 }
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131 ],
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132 "position": {
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133 "left": 892,
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134 "top": 415
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135 },
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136 "post_job_actions": {},
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137 "tool_errors": null,
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138 "tool_id": "Cut1",
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139 "tool_state": "{\"columnList\": \"\\\"c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": 0}",
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140 "tool_version": "1.0.1",
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141 "type": "tool",
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142 "user_outputs": []
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143 },
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144 "5": {
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145 "annotation": "",
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146 "id": 5,
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147 "input_connections": {
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148 "inputSNPfile": {
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149 "id": 2,
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150 "output_name": "outputfile"
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151 },
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152 "inputTargetfile": {
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153 "id": 4,
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154 "output_name": "out_file1"
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155 },
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156 "inputfastaFile": {
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157 "id": 0,
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158 "output_name": "output"
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159 }
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160 },
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161 "inputs": [
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162 {
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163 "description": "runtime parameter for tool Design primers to features",
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164 "name": "min_size"
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165 },
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166 {
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167 "description": "runtime parameter for tool Design primers to features",
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168 "name": "max_size"
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169 }
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170 ],
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171 "name": "Design primers to features",
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172 "outputs": [
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173 {
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174 "name": "primer_outputfile",
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175 "type": "tabular"
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176 }
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
177 ],
be070a68521e Uploaded workflow from vcf file to CAPS
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diff changeset
178 "position": {
be070a68521e Uploaded workflow from vcf file to CAPS
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179 "left": 1186,
be070a68521e Uploaded workflow from vcf file to CAPS
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180 "top": 382
be070a68521e Uploaded workflow from vcf file to CAPS
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181 },
be070a68521e Uploaded workflow from vcf file to CAPS
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diff changeset
182 "post_job_actions": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
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diff changeset
183 "RenameDatasetActionprimer_outputfile": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
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diff changeset
184 "action_arguments": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
185 "newname": "PrimerPairs"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
186 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
187 "action_type": "RenameDatasetAction",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
188 "output_name": "primer_outputfile"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
189 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
190 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
191 "tool_errors": null,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
192 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/Genetic_Marker_Design_2/1.0.0",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
193 "tool_state": "{\"__page__\": 0, \"inputTargetfile\": \"null\", \"inputfastaFile\": \"null\", \"min_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"inputSNPfile\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"max_size\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
194 "tool_version": "1.0.0",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
195 "type": "tool",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
196 "user_outputs": []
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
197 },
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
198 "6": {
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
199 "annotation": "",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
200 "id": 6,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
201 "input_connections": {
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
202 "input": {
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
203 "id": 5,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
204 "output_name": "primer_outputfile"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
205 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
206 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
207 "inputs": [],
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
208 "name": "Select",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
209 "outputs": [
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
210 {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
211 "name": "out_file1",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
212 "type": "input"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
213 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
214 ],
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
215 "position": {
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
216 "left": 1406,
be070a68521e Uploaded workflow from vcf file to CAPS
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parents:
diff changeset
217 "top": 382
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
218 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
219 "post_job_actions": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
220 "RenameDatasetActionout_file1": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
221 "action_arguments": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
222 "newname": "SuccessfulDesignSets"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
223 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
224 "action_type": "RenameDatasetAction",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
225 "output_name": "out_file1"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
226 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
227 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
228 "tool_errors": null,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
229 "tool_id": "Grep1",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
230 "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"invert\": \"\\\"true\\\"\", \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"pattern\": \"\\\"NONE\\\"\"}",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
231 "tool_version": "1.0.1",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
232 "type": "tool",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
233 "user_outputs": []
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
234 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
235 "7": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
236 "annotation": "",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
237 "id": 7,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
238 "input_connections": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
239 "inputFile": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
240 "id": 6,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
241 "output_name": "out_file1"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
242 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
243 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
244 "inputs": [],
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
245 "name": "Unique",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
246 "outputs": [
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
247 {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
248 "name": "outputfile",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
249 "type": "txt"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
250 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
251 ],
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
252 "position": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
253 "left": 1625.9999389648438,
be070a68521e Uploaded workflow from vcf file to CAPS
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diff changeset
254 "top": 382
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
255 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
256 "post_job_actions": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
257 "RenameDatasetActionoutputfile": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
258 "action_arguments": {
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
259 "newname": "UniquePrimerSets"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
260 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
261 "action_type": "RenameDatasetAction",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
262 "output_name": "outputfile"
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
263 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
264 },
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
265 "tool_errors": null,
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
266 "tool_id": "toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers/uni_Mask_1/1.0.0",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
267 "tool_state": "{\"__page__\": 0, \"chromInfo\": \"\\\"/opt/galaxy_workflow/galaxy-pfr-production-2/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
268 "tool_version": "1.0.0",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
269 "type": "tool",
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
270 "user_outputs": []
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
271 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
272 }
be070a68521e Uploaded workflow from vcf file to CAPS
john-mccallum
parents:
diff changeset
273 }