Mercurial > repos > nml > mob_suite

annotate workflows/AMRworkflow_STARAMR.ga @ 5:09424ec94e80 draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit e3f242a0dbf429ac0394b6962441aaef367645a8"
author nml
date Wed, 13 Nov 2019 14:09:11 -0500
parents 066b2a1c6a55
children
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1 {
3
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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)",
2
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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106 },
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107 {
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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108 "name": "resfinder",
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109 "type": "tabular"
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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110 },
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111 {
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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118 },
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119 {
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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120 "name": "excel",
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121 "type": "xlsx"
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122 }
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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139 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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\\\"}\"}",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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156 },
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157 {
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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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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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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166 },
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2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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167 {
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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168 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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169 "output_name": "summary",
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170 "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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171 }
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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172 ]
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
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173 }
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066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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174 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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parents: 2
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175 "tags": [
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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176 "AMR",
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177 "Resistance",
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178 "ResFinder",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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179 "StarAMR",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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parents: 2
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180 "MOB-Suite",
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parents: 2
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181 "ARGs"
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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182 ],
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
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parents: 2
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183 "uuid": "d6ce87c0-2d16-4c8c-bea8-6464264565d4"
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184 }