Mercurial > repos > nml > mob_suite
changeset 3:066b2a1c6a55 draft
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
| author | nml |
|---|---|
| date | Mon, 20 Aug 2018 15:04:54 -0400 |
| parents | 2c7f721a4905 |
| children | 1c5dfecfbb4d |
| files | mob_recon.xml workflows/AMRworkflow_STARAMR.ga |
| diffstat | 2 files changed, 110 insertions(+), 91 deletions(-) [+] |
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--- a/mob_recon.xml Fri Aug 17 11:12:08 2018 -0400 +++ b/mob_recon.xml Mon Aug 20 15:04:54 2018 -0400 @@ -96,7 +96,7 @@ **Workflow** - There is a preliminary Mobilome and Resistome Analysis Workflow linking mob_recon with staramr providing reports on mobilome and resistome https://github.com/phac-nml/mob-suite/. +This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be mamanually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga. -----
--- a/workflows/AMRworkflow_STARAMR.ga Fri Aug 17 11:12:08 2018 -0400 +++ b/workflows/AMRworkflow_STARAMR.ga Mon Aug 20 15:04:54 2018 -0400 @@ -1,165 +1,184 @@ { - "a_galaxy_workflow": "true", - "annotation": "", - "format-version": "0.1", - "name": "AMRworkflow", + "a_galaxy_workflow": "true", + "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", + "format-version": "0.1", + "name": "Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR)", "steps": { "0": { - "annotation": "", - "content_id": "mob_recon", - "errors": null, - "id": 0, - "input_connections": {}, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8", + "errors": null, + "id": 0, + "input_connections": {}, "inputs": [ { - "description": "runtime parameter for tool MOB-Recon", + "description": "runtime parameter for tool MOB-Recon", "name": "input" } - ], - "label": null, - "name": "MOB-Recon", + ], + "label": null, + "name": "MOB-Recon", "outputs": [ { - "name": "seqhits", + "name": "seqhits", "type": "input" - }, + }, { - "name": "outfile1", + "name": "outfile1", "type": "tabular" - }, + }, { - "name": "outfile2", + "name": "outfile2", "type": "tabular" - }, + }, { - "name": "outfile3", + "name": "outfile3", "type": "tabular" } - ], + ], "position": { - "left": 200, + "left": 200, "top": 200 - }, + }, "post_job_actions": { "HideDatasetActionoutfile1": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "outfile1" - }, + }, "HideDatasetActionoutfile2": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "outfile2" - }, + }, "HideDatasetActionoutfile3": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "outfile3" } - }, - "tool_id": "mob_recon", - "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}", - "tool_version": "1.4.8", - "type": "tool", - "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1", + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8", + "tool_shed_repository": { + "changeset_revision": "2c7f721a4905", + "name": "mob_suite", + "owner": "nml", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "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}", + "tool_version": "1.4.8", + "type": "tool", + "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1", "workflow_outputs": [ { - "label": null, - "output_name": "seqhits", + "label": null, + "output_name": "seqhits", "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433" } ] - }, + }, "1": { - "annotation": "", - "content_id": "staramr_search", - "errors": null, - "id": 1, + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.2.2", + "errors": null, + "id": 1, "input_connections": { "genomes": { - "id": 0, + "id": 0, "output_name": "seqhits" } - }, + }, "inputs": [ { - "description": "runtime parameter for tool staramr", + "description": "runtime parameter for tool staramr", "name": "genomes" } - ], - "label": null, - "name": "staramr", + ], + "label": null, + "name": "staramr", "outputs": [ { - "name": "blast_hits", + "name": "blast_hits", "type": "input" - }, + }, { - "name": "summary", + "name": "summary", "type": "tabular" - }, + }, { - "name": "resfinder", + "name": "resfinder", "type": "tabular" - }, + }, { - "name": "pointfinder", + "name": "pointfinder", "type": "tabular" - }, + }, { - "name": "settings", + "name": "settings", "type": "txt" - }, + }, { - "name": "excel", + "name": "excel", "type": "xlsx" } - ], + ], "position": { - "left": 420, + "left": 420, "top": 200 - }, + }, "post_job_actions": { "HideDatasetActionpointfinder": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "pointfinder" - }, + }, "HideDatasetActionsettings": { - "action_arguments": {}, - "action_type": "HideDatasetAction", + "action_arguments": {}, + "action_type": "HideDatasetAction", "output_name": "settings" } - }, - "tool_id": "staramr_search", - "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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