Mercurial > repos > dfornika > mob_suite

annotate workflows/AMRworkflow_STARAMR.ga @ 23:9fb816e94615 draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty
author dfornika
date Mon, 23 Sep 2019 20:23:42 -0400
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1 {
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2 "a_galaxy_workflow": "true",
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3 "annotation": "Mobilome and resistome analyses are valuable tools to better characterize genome assemblies for the presence of antibiotic resistance phenotypes and mobile elements such as plasmids. The location of the resistance (chromosome or plasmid) will provide information on potential dissemination potential of the antibiotic resistance genes via horizontal or clonal gene transfer mechanisms (available via the summary.tsv report). This draft workflow will help end-user to potentially qualitatively estimate potential AMR risk for a given isolate along with the underlying mechanisms and the epidemiology of antimicrobial resistance. \n\nPlease provide us with your feedback in order to improve usability and flexibility of the workflow. For more information refer to http://dx.doi.org/10.1099/mgen.0.000206 and https://github.com/phac-nml/staramr. \n\n",
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4 "format-version": "0.1",
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5 "name": "Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR)",
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6 "steps": {
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7 "0": {
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8 "annotation": "",
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9 "content_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8",
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10 "errors": null,
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11 "id": 0,
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12 "input_connections": {},
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13 "inputs": [
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14 {
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15 "description": "runtime parameter for tool MOB-Recon",
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16 "name": "input"
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17 }
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18 ],
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19 "label": null,
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20 "name": "MOB-Recon",
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21 "outputs": [
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22 {
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23 "name": "seqhits",
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24 "type": "input"
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25 },
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26 {
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27 "name": "outfile1",
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28 "type": "tabular"
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29 },
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30 {
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31 "name": "outfile2",
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32 "type": "tabular"
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33 },
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34 {
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35 "name": "outfile3",
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36 "type": "tabular"
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37 }
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38 ],
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39 "position": {
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40 "left": 200,
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41 "top": 200
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42 },
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43 "post_job_actions": {
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44 "HideDatasetActionoutfile1": {
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45 "action_arguments": {},
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46 "action_type": "HideDatasetAction",
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47 "output_name": "outfile1"
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48 },
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49 "HideDatasetActionoutfile2": {
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50 "action_arguments": {},
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51 "action_type": "HideDatasetAction",
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52 "output_name": "outfile2"
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53 },
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54 "HideDatasetActionoutfile3": {
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55 "action_arguments": {},
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56 "action_type": "HideDatasetAction",
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57 "output_name": "outfile3"
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58 }
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59 },
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60 "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8",
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61 "tool_shed_repository": {
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62 "changeset_revision": "2c7f721a4905",
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63 "name": "mob_suite",
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64 "owner": "nml",
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65 "tool_shed": "toolshed.g2.bx.psu.edu"
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66 },
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67 "tool_state": "{\"adv_param\": \"{\\\"min_length_condition\\\": {\\\"min_length_param\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"min_con_ident\\\": \\\"80\\\", \\\"min_mob_ident\\\": \\\"80\\\", \\\"min_mob_evalue\\\": \\\"1e-05\\\", \\\"min_rep_evalue\\\": \\\"1e-05\\\", \\\"unicycler_contigs\\\": \\\"True\\\", \\\"min_rep_ident\\\": \\\"80\\\", \\\"min_rpp_evalue\\\": \\\"1e-05\\\", \\\"min_rpp_ident\\\": \\\"80\\\", \\\"run_circlator\\\": \\\"True\\\", \\\"min_con_evalue\\\": \\\"1e-05\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": null}",
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68 "tool_version": "1.4.8",
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69 "type": "tool",
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70 "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1",
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71 "workflow_outputs": [
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72 {
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73 "label": null,
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74 "output_name": "seqhits",
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75 "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433"
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76 }
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77 ]
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78 },
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79 "1": {
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80 "annotation": "",
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81 "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.2.2",
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82 "errors": null,
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83 "id": 1,
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84 "input_connections": {
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85 "genomes": {
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86 "id": 0,
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87 "output_name": "seqhits"
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88 }
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89 },
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90 "inputs": [
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91 {
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92 "description": "runtime parameter for tool staramr",
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93 "name": "genomes"
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94 }
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95 ],
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96 "label": null,
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97 "name": "staramr",
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98 "outputs": [
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99 {
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100 "name": "blast_hits",
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101 "type": "input"
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102 },
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103 {
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104 "name": "summary",
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105 "type": "tabular"
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106 },
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107 {
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108 "name": "resfinder",
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109 "type": "tabular"
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110 },
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111 {
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112 "name": "pointfinder",
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113 "type": "tabular"
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114 },
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115 {
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116 "name": "settings",
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117 "type": "txt"
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118 },
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119 {
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120 "name": "excel",
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121 "type": "xlsx"
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122 }
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123 ],
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124 "position": {
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125 "left": 420,
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126 "top": 200
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127 },
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128 "post_job_actions": {
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129 "HideDatasetActionpointfinder": {
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130 "action_arguments": {},
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131 "action_type": "HideDatasetAction",
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132 "output_name": "pointfinder"
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133 },
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134 "HideDatasetActionsettings": {
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135 "action_arguments": {},
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136 "action_type": "HideDatasetAction",
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137 "output_name": "settings"
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138 }
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139 },
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140 "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.2.2",
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141 "tool_shed_repository": {
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142 "changeset_revision": "9047a1d3d8ea",
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143 "name": "staramr",
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144 "owner": "nml",
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145 "tool_shed": "toolshed.g2.bx.psu.edu"
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146 },
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147 "tool_state": "{\"__page__\": null, \"use_pointfinder\": \"{\\\"enable\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genomes\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"pid_threshold\\\": \\\"98.0\\\", \\\"exclude_resistance_phenotypes\\\": \\\"false\\\", \\\"exclude_negatives\\\": \\\"false\\\", \\\"plength_resfinder\\\": \\\"60.0\\\", \\\"plength_pointfinder\\\": \\\"95.0\\\", \\\"report_all_blast\\\": \\\"false\\\"}\"}",
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148 "tool_version": "0.2.2",
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149 "type": "tool",
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150 "uuid": "41f8718f-87a0-45d2-b79d-e5afddea1532",
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151 "workflow_outputs": [
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152 {
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153 "label": null,
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154 "output_name": "blast_hits",
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155 "uuid": "9e8592ad-71c0-4528-8e8b-efcd3bb9183a"
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156 },
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157 {
9fb816e94615 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty
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158 "label": null,
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159 "output_name": "resfinder",
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160 "uuid": "2f27a46b-29bf-4abf-9d26-fce4e9fc9dd5"
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161 },
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162 {
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163 "label": null,
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164 "output_name": "excel",
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165 "uuid": "67549d0b-0480-4c25-8bfd-1fa78cfdb066"
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166 },
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167 {
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168 "label": null,
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169 "output_name": "summary",
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170 "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7"
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171 }
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172 ]
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173 }
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174 },
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175 "tags": [
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176 "AMR",
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177 "Resistance",
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178 "ResFinder",
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179 "StarAMR",
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180 "MOB-Suite",
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181 "ARGs"
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182 ],
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183 "uuid": "d6ce87c0-2d16-4c8c-bea8-6464264565d4"
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184 }