annotate amrplusplus_workflow.ga @ 8:0eae27b15aa0 draft default tip

planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
author chrisd
date Thu, 14 Jul 2016 19:04:32 -0400
parents 0b7210ad9187
children
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1 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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2 "a_galaxy_workflow": "true",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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3 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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4 "format-version": "0.1",
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5 "name": "amrplusplus workflow (imported from uploaded file)",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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6 "steps": {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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8 "annotation": "",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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11 "input_connections": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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12 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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13 {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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15 "name": "FASTQ Forward"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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16 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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17 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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18 "label": "FASTQ Forward",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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19 "name": "Input dataset",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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20 "outputs": [],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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24 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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27 "tool_state": "{\"name\": \"FASTQ Forward\"}",
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28 "tool_version": null,
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29 "type": "data_input",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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31 "workflow_outputs": [
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32 {
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34 "output_name": "output",
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36 }
0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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37 ]
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38 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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40 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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43 "input_connections": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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44 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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45 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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46 "description": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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47 "name": "FASTQ Reverse"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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48 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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49 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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50 "label": "FASTQ Reverse",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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51 "name": "Input dataset",
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52 "outputs": [],
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56 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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59 "tool_state": "{\"name\": \"FASTQ Reverse\"}",
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60 "tool_version": null,
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61 "type": "data_input",
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62 "uuid": "a24ee7c0-b919-4426-8866-7d9939536e12",
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63 "workflow_outputs": [
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64 {
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65 "label": null,
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66 "output_name": "output",
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68 }
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72 "annotation": "",
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75 "input_connections": {},
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76 "inputs": [
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77 {
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78 "description": "",
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79 "name": "Host Genome"
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80 }
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81 ],
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82 "label": "Host Genome",
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83 "name": "Input dataset",
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84 "outputs": [],
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85 "position": {
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88 },
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91 "tool_state": "{\"name\": \"Host Genome\"}",
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92 "tool_version": null,
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93 "type": "data_input",
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94 "uuid": "96c8f450-cb64-4641-884a-c1dabceeff5d",
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95 "workflow_outputs": [
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96 {
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97 "label": null,
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98 "output_name": "output",
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100 }
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101 ]
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102 },
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104 "annotation": "",
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105 "content_id": null,
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106 "id": 3,
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107 "input_connections": {},
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108 "inputs": [
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109 {
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110 "description": "",
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111 "name": "AMR Database"
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112 }
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113 ],
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114 "label": "AMR Database",
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115 "name": "Input dataset",
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116 "outputs": [],
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117 "position": {
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118 "left": 1086,
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119 "top": 560
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120 },
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121 "tool_errors": null,
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122 "tool_id": null,
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123 "tool_state": "{\"name\": \"AMR Database\"}",
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124 "tool_version": null,
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125 "type": "data_input",
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126 "uuid": "2615ede9-3d0a-422b-b04d-829157475d47",
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127 "workflow_outputs": [
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128 {
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129 "label": null,
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130 "output_name": "output",
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131 "uuid": "32fcc9ba-8864-4fa7-a337-917a9612844a"
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132 }
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133 ]
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134 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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135 "4": {
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136 "annotation": "",
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137 "content_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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138 "id": 4,
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139 "input_connections": {
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140 "paired_end|paired_input_type_conditional|fastq_r1_in": {
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141 "id": 0,
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142 "output_name": "output"
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143 },
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144 "paired_end|paired_input_type_conditional|fastq_r2_in": {
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145 "id": 1,
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146 "output_name": "output"
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147 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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148 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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149 "inputs": [],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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150 "label": null,
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151 "name": "Trimmomatic",
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152 "outputs": [
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153 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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154 "name": "fastq_out_paired",
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155 "type": "input"
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156 },
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157 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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158 "name": "fastq_out_unpaired",
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159 "type": "input"
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160 },
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161 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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162 "name": "fastq_out_r1_paired",
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163 "type": "fastqsanger"
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164 },
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165 {
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166 "name": "fastq_out_r2_paired",
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167 "type": "fastqsanger"
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168 },
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169 {
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170 "name": "fastq_out_r1_unpaired",
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171 "type": "fastqsanger"
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172 },
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173 {
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174 "name": "fastq_out_r2_unpaired",
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175 "type": "fastqsanger"
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176 },
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177 {
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178 "name": "fastq_out",
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179 "type": "fastqsanger"
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180 }
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181 ],
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182 "position": {
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183 "left": 465,
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184 "top": 303
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185 },
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186 "post_job_actions": {
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187 "HideDatasetActionfastq_out": {
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188 "action_arguments": {},
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189 "action_type": "HideDatasetAction",
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190 "output_name": "fastq_out"
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191 },
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192 "HideDatasetActionfastq_out_paired": {
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193 "action_arguments": {},
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194 "action_type": "HideDatasetAction",
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195 "output_name": "fastq_out_paired"
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196 },
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197 "HideDatasetActionfastq_out_r1_unpaired": {
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198 "action_arguments": {},
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199 "action_type": "HideDatasetAction",
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200 "output_name": "fastq_out_r1_unpaired"
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201 },
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202 "HideDatasetActionfastq_out_r2_unpaired": {
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203 "action_arguments": {},
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204 "action_type": "HideDatasetAction",
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205 "output_name": "fastq_out_r2_unpaired"
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206 },
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207 "HideDatasetActionfastq_out_unpaired": {
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208 "action_arguments": {},
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209 "action_type": "HideDatasetAction",
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210 "output_name": "fastq_out_unpaired"
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211 }
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212 },
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213 "tool_errors": null,
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214 "tool_id": "toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3",
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215 "tool_shed_repository": {
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216 "changeset_revision": "f8a9a5eaca8a",
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217 "name": "trimmomatic",
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218 "owner": "pjbriggs",
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219 "tool_shed": "toolshed.g2.bx.psu.edu"
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220 },
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221 "tool_state": "{\"operations\": \"[{\\\"__index__\\\": 0, \\\"operation\\\": {\\\"window_size\\\": \\\"4\\\", \\\"name\\\": \\\"SLIDINGWINDOW\\\", \\\"__current_case__\\\": 0, \\\"required_quality\\\": \\\"20\\\"}}]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"paired_end\": \"{\\\"is_paired_end\\\": \\\"true\\\", \\\"paired_input_type_conditional\\\": {\\\"paired_input_type\\\": \\\"pair_of_files\\\", \\\"fastq_r1_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"fastq_r2_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}, \\\"__current_case__\\\": 1}\", \"illuminaclip\": \"{\\\"do_illuminaclip\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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222 "tool_version": "0.32.3",
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223 "type": "tool",
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224 "uuid": "c943ae63-aa6c-4d42-9088-b08335b8b6c6",
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225 "workflow_outputs": [
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226 {
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227 "label": null,
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228 "output_name": "fastq_out_r1_paired",
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229 "uuid": "e5cb04a2-09b6-41e5-b93d-54c4c6c8e488"
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230 },
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231 {
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232 "label": null,
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233 "output_name": "fastq_out_r2_paired",
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234 "uuid": "ada191c5-9f20-4052-aa5e-03f73f9587ad"
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235 }
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236 ]
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237 },
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238 "5": {
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239 "annotation": "",
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240 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0",
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241 "id": 5,
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242 "input_connections": {
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243 "reference": {
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244 "id": 3,
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245 "output_name": "output"
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246 }
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247 },
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248 "inputs": [
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249 {
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250 "description": "runtime parameter for tool MetaSNP",
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251 "name": "sam_type"
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252 },
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253 {
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254 "description": "runtime parameter for tool MetaSNP",
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255 "name": "reference"
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256 }
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257 ],
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258 "label": null,
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259 "name": "MetaSNP",
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260 "outputs": [
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261 {
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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262 "name": "output",
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263 "type": "tabular"
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264 }
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265 ],
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266 "position": {
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267 "left": 1447,
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268 "top": 543
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269 },
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270 "post_job_actions": {},
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271 "tool_errors": null,
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272 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/0.1.0",
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273 "tool_shed_repository": {
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274 "changeset_revision": "a3d1f2a85806",
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275 "name": "metasnp",
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276 "owner": "chrisd",
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277 "tool_shed": "toolshed.g2.bx.psu.edu"
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278 },
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279 "tool_state": "{\"sam_type\": \"{\\\"best\\\": \\\"false\\\", \\\"sampe_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"mode\\\": \\\"paired_end\\\", \\\"__current_case__\\\": 1}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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280 "tool_version": "0.1.0",
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281 "type": "tool",
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282 "uuid": "f126b5ac-a201-4478-8336-cdc6d70c54ca",
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283 "workflow_outputs": [
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284 {
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285 "label": null,
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286 "output_name": "output",
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287 "uuid": "2a7f2c96-ce1d-4ce0-b8cb-ba31df13bdb6"
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288 }
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289 ]
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290 },
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291 "6": {
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292 "annotation": "",
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293 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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294 "id": 6,
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295 "input_connections": {
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296 "input_type|fastq_input1": {
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297 "id": 4,
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298 "output_name": "fastq_out_r1_paired"
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299 },
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300 "input_type|fastq_input2": {
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301 "id": 4,
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302 "output_name": "fastq_out_r2_paired"
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303 },
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304 "reference_source|ref_file": {
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305 "id": 2,
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306 "output_name": "output"
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307 }
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308 },
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309 "inputs": [
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310 {
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311 "description": "runtime parameter for tool Map with BWA",
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312 "name": "input_type"
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313 },
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314 {
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315 "description": "runtime parameter for tool Map with BWA",
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316 "name": "input_type"
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317 },
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318 {
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319 "description": "runtime parameter for tool Map with BWA",
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320 "name": "reference_source"
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321 }
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322 ],
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323 "label": null,
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324 "name": "Map with BWA",
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325 "outputs": [
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326 {
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327 "name": "bam_output",
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328 "type": "bam"
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329 }
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330 ],
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331 "position": {
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332 "left": 772.5,
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333 "top": 306
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334 },
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335 "post_job_actions": {},
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336 "tool_errors": null,
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337 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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338 "tool_shed_repository": {
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339 "changeset_revision": "546ada4a9f43",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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340 "name": "bwa",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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341 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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342 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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343 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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345 "tool_version": "0.7.12.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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346 "type": "tool",
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diff changeset
347 "uuid": "3c509fb7-aef9-4e6d-bbb7-f6099d71f15e",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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348 "workflow_outputs": [
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349 {
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350 "label": null,
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351 "output_name": "bam_output",
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353 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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354 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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355 },
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356 "7": {
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357 "annotation": "",
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358 "content_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1",
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360 "input_connections": {
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361 "input": {
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362 "id": 6,
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chrisd
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363 "output_name": "bam_output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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364 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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365 },
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366 "inputs": [
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367 {
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368 "description": "runtime parameter for tool Samtools flag_filter",
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369 "name": "input"
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370 }
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371 ],
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372 "label": null,
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373 "name": "Samtools flag_filter",
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374 "outputs": [
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375 {
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376 "name": "output",
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377 "type": "bam"
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378 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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379 ],
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380 "position": {
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381 "left": 1004.5,
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chrisd
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382 "top": 303
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383 },
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384 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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385 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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386 "tool_id": "toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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387 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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388 "changeset_revision": "97bb72be07f9",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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389 "name": "samtools_flag_filter_1_2",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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390 "owner": "brenninc",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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391 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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392 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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393 "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"bits\": \"[{\\\"__index__\\\": 0, \\\"flag\\\": \\\"0x0004\\\", \\\"state\\\": \\\"f\\\"}]\", \"__page__\": 0}",
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394 "tool_version": "0.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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395 "type": "tool",
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diff changeset
396 "uuid": "e31b4dcc-9623-4c50-8139-214e40fe29d0",
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397 "workflow_outputs": [
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diff changeset
398 {
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399 "label": null,
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400 "output_name": "output",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
401 "uuid": "c9c36760-d2a9-4c05-808c-05a092260670"
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402 }
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403 ]
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diff changeset
404 },
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diff changeset
405 "8": {
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diff changeset
406 "annotation": "",
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407 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
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diff changeset
408 "id": 8,
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diff changeset
409 "input_connections": {
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410 "input_type|bam_input": {
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diff changeset
411 "id": 7,
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diff changeset
412 "output_name": "output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
413 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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414 "reference_source|ref_file": {
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diff changeset
415 "id": 3,
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diff changeset
416 "output_name": "output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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417 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
418 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
419 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
420 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
421 "description": "runtime parameter for tool Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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422 "name": "input_type"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
423 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
425 "description": "runtime parameter for tool Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
426 "name": "reference_source"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
427 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
428 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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429 "label": null,
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chrisd
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diff changeset
430 "name": "Map with BWA",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
431 "outputs": [
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chrisd
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diff changeset
432 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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433 "name": "bam_output",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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434 "type": "bam"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
435 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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436 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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437 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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438 "left": 1279.5,
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chrisd
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439 "top": 305
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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440 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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441 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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442 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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443 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
444 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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445 "changeset_revision": "546ada4a9f43",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
446 "name": "bwa",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
447 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
448 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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449 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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450 "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"bam_input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 3, \\\"input_type_selector\\\": \\\"paired_bam\\\", \\\"adv_bam_pe_options\\\": {\\\"__current_case__\\\": 1, \\\"adv_pe_options_selector\\\": \\\"do_not_set\\\"}}\", \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
451 "tool_version": "0.7.12.1",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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452 "type": "tool",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
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diff changeset
453 "uuid": "4dff04dd-4331-4390-a21d-64140a177ce4",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
454 "workflow_outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
455 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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456 "label": null,
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chrisd
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diff changeset
457 "output_name": "bam_output",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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diff changeset
458 "uuid": "341955c7-7ae9-4872-a52a-f6b2f298cba1"
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
459 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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460 ]
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
461 },
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diff changeset
462 "9": {
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
463 "annotation": "",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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464 "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0",
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chrisd
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diff changeset
465 "id": 9,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
466 "input_connections": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
467 "input1": {
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
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diff changeset
468 "id": 8,
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
469 "output_name": "bam_output"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
470 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
471 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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472 "inputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
473 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
474 "description": "runtime parameter for tool Sort",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
475 "name": "input1"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
476 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
477 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
478 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
479 "name": "Sort",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
480 "outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
481 {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
482 "name": "output1",
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chrisd
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diff changeset
483 "type": "bam"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
484 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
485 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
486 "position": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
487 "left": 1506,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
488 "top": 306
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
489 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
490 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
491 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
492 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
493 "tool_shed_repository": {
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
494 "changeset_revision": "a430da4f04cd",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
495 "name": "samtools_sort",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
496 "owner": "devteam",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
497 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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498 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
499 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sort_mode\": \"\\\"-n\\\"\"}",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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diff changeset
500 "tool_version": "2.0",
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chrisd
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diff changeset
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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503 "workflow_outputs": [
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chrisd
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chrisd
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510 },
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chrisd
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chrisd
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chrisd
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
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chrisd
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518 "output_name": "output1"
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chrisd
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chrisd
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520 },
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chrisd
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522 {
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chrisd
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524 "name": "input1"
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chrisd
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chrisd
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chrisd
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chrisd
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528 "name": "BAM-to-SAM",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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chrisd
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530 {
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chrisd
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chrisd
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532 "type": "sam"
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chrisd
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chrisd
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chrisd
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chrisd
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536 "left": 1507.5,
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chrisd
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chrisd
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538 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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539 "post_job_actions": {},
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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540 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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541 "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0",
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chrisd
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542 "tool_shed_repository": {
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chrisd
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543 "changeset_revision": "af7c50162f0b",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
544 "name": "bam_to_sam",
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chrisd
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diff changeset
545 "owner": "devteam",
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chrisd
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diff changeset
546 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
diff changeset
547 },
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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diff changeset
548 "tool_state": "{\"header\": \"\\\"-h\\\"\", \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": 0}",
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chrisd
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diff changeset
549 "tool_version": "2.0",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
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550 "type": "tool",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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diff changeset
551 "uuid": "5196c387-3fad-46dc-9e6f-63af7ffae562",
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chrisd
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552 "workflow_outputs": [
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chrisd
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553 {
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chrisd
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chrisd
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555 "output_name": "output1",
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0b7210ad9187 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 40ce29d55ffc7141cb9a62c4d9bd03cd8fc17915-dirty
chrisd
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diff changeset
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chrisd
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diff changeset
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chrisd
parents: 6
diff changeset
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chrisd
parents: 6
diff changeset
559 },
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chrisd
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560 "11": {
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chrisd
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561 "annotation": "",
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chrisd
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562 "content_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
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chrisd
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563 "id": 11,
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chrisd
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564 "input_connections": {
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chrisd
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diff changeset
565 "reference": {
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chrisd
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chrisd
parents:
diff changeset
567 "output_name": "output"
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chrisd
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568 },
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chrisd
parents: 7
diff changeset
569 "sam": {
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chrisd
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diff changeset
570 "id": 10,
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chrisd
parents:
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571 "output_name": "output1"
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chrisd
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diff changeset
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chrisd
parents:
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573 },
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chrisd
parents:
diff changeset
574 "inputs": [
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chrisd
parents:
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575 {
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chrisd
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576 "description": "runtime parameter for tool Coverage Sampler",
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
diff changeset
577 "name": "reference"
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chrisd
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578 },
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chrisd
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579 {
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chrisd
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580 "description": "runtime parameter for tool Coverage Sampler",
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
diff changeset
581 "name": "sam"
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chrisd
parents:
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chrisd
parents:
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chrisd
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diff changeset
584 "label": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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585 "name": "Coverage Sampler",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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586 "outputs": [
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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587 {
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chrisd
parents: 7
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588 "name": "output",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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589 "type": "tabular"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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590 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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591 ],
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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592 "position": {
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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593 "left": 1631.5,
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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594 "top": 545
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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595 },
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0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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596 "post_job_actions": {},
5
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chrisd
parents:
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597 "tool_errors": null,
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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598 "tool_id": "toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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599 "tool_shed_repository": {
8
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parents: 7
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600 "changeset_revision": "ec439b0e7512",
5
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chrisd
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601 "name": "coverage_sampler",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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602 "owner": "chrisd",
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
chrisd
parents:
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603 "tool_shed": "toolshed.g2.bx.psu.edu"
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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604 },
8
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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parents: 7
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605 "tool_state": "{\"__page__\": 0, \"reference\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sam\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"min\": \"\\\"5\\\"\", \"max\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"samples\": \"\\\"1\\\"\", \"skip\": \"\\\"5\\\"\", \"threshold\": \"\\\"80\\\"\"}",
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04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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606 "tool_version": "0.1.0",
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607 "type": "tool",
8
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parents: 7
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608 "uuid": "a74c17eb-f115-40b3-847d-03b89c251bc7",
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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609 "workflow_outputs": [
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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610 {
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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611 "label": null,
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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parents: 7
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612 "output_name": "output",
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
chrisd
parents: 7
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613 "uuid": "57902fb4-a733-4429-8dfd-905ad0dd2f03"
0eae27b15aa0 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit 5e58b41d1ef7243f07d32905bd822d0a13876344-dirty
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parents: 7
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614 }
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615 ]
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616 }
04f9c20fecf8 planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/workflows/amrplusplus commit c9b00ed961b62f1825feeeb757c283c949a9bce9-dirty
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parents:
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617 },
8
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parents: 7
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618 "uuid": "9ed4d064-e299-406d-a56f-e7eec8120829"
7
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parents: 6
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619 }