diff workflows/AMRworkflow_STARAMR.ga @ 2:2c7f721a4905 draft

planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflows/AMRworkflow_STARAMR.ga	Fri Aug 17 11:12:08 2018 -0400
@@ -0,0 +1,165 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "format-version": "0.1",
+    "name": "AMRworkflow",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": "mob_recon",
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MOB-Recon",
+                    "name": "input"
+                }
+            ],
+            "label": null,
+            "name": "MOB-Recon",
+            "outputs": [
+                {
+                    "name": "seqhits",
+                    "type": "input"
+                },
+                {
+                    "name": "outfile1",
+                    "type": "tabular"
+                },
+                {
+                    "name": "outfile2",
+                    "type": "tabular"
+                },
+                {
+                    "name": "outfile3",
+                    "type": "tabular"
+                }
+            ],
+            "position": {
+                "left": 200,
+                "top": 200
+            },
+            "post_job_actions": {
+                "HideDatasetActionoutfile1": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "outfile1"
+                },
+                "HideDatasetActionoutfile2": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "outfile2"
+                },
+                "HideDatasetActionoutfile3": {
+                    "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",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "seqhits",
+                    "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "staramr_search",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "genomes": {
+                    "id": 0,
+                    "output_name": "seqhits"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool staramr",
+                    "name": "genomes"
+                }
+            ],
+            "label": null,
+            "name": "staramr",
+            "outputs": [
+                {
+                    "name": "blast_hits",
+                    "type": "input"
+                },
+                {
+                    "name": "summary",
+                    "type": "tabular"
+                },
+                {
+                    "name": "resfinder",
+                    "type": "tabular"
+                },
+                {
+                    "name": "pointfinder",
+                    "type": "tabular"
+                },
+                {
+                    "name": "settings",
+                    "type": "txt"
+                },
+                {
+                    "name": "excel",
+                    "type": "xlsx"
+                }
+            ],
+            "position": {
+                "left": 420,
+                "top": 200
+            },
+            "post_job_actions": {
+                "HideDatasetActionpointfinder": {
+                    "action_arguments": {},
+                    "action_type": "HideDatasetAction",
+                    "output_name": "pointfinder"
+                },
+                "HideDatasetActionsettings": {
+                    "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\\\"}\"}",
+            "tool_version": "0.2.2",
+            "type": "tool",
+            "uuid": "41f8718f-87a0-45d2-b79d-e5afddea1532",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "blast_hits",
+                    "uuid": "9e8592ad-71c0-4528-8e8b-efcd3bb9183a"
+                },
+                {
+                    "label": null,
+                    "output_name": "resfinder",
+                    "uuid": "2f27a46b-29bf-4abf-9d26-fce4e9fc9dd5"
+                },
+                {
+                    "label": null,
+                    "output_name": "excel",
+                    "uuid": "67549d0b-0480-4c25-8bfd-1fa78cfdb066"
+                },
+                {
+                    "label": null,
+                    "output_name": "summary",
+                    "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "4c695847-5fc7-4020-a125-a500700ab320"
+}