Repository 'mgsfast'
hg clone https://toolshed.g2.bx.psu.edu/repos/ntino/mgsfast

Changeset 0:8f9b6edb6240 (2018-05-05)
Commit message:
Uploaded
added:
Galaxy-Workflow-MGS-Fast_pipeline.ga
b
diff -r 000000000000 -r 8f9b6edb6240 Galaxy-Workflow-MGS-Fast_pipeline.ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-MGS-Fast_pipeline.ga Sat May 05 12:47:57 2018 -0400
[
b'@@ -0,0 +1,597 @@\n+{\n+    "a_galaxy_workflow": "true", \n+    "annotation": "", \n+    "format-version": "0.1", \n+    "name": "Parallel MGS-Fast pipeline\'", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "MGS Paired-End Reads 1"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 207.03125, \n+                "top": 440.984375\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"MGS Paired-End Reads 1\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "user_outputs": [], \n+            "uuid": "590833d5-cf50-4080-aca8-09bf60edf9cb"\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "id": 1, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "MGS Paired-End Reads 2"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset", \n+            "outputs": [], \n+            "position": {\n+                "left": 200, \n+                "top": 523.96875\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"name\\": \\"MGS Paired-End Reads 2\\"}", \n+            "tool_version": null, \n+            "type": "data_input", \n+            "user_outputs": [], \n+            "uuid": "c98deb39-dcfc-49ff-a087-d279e3a6f6ea"\n+        }, \n+        "2": {\n+            "annotation": "", \n+            "id": 2, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FastQC", \n+            "outputs": [\n+                {\n+                    "name": "html_file", \n+                    "type": "html"\n+                }, \n+                {\n+                    "name": "text_file", \n+                    "type": "txt"\n+                }\n+            ], \n+            "position": {\n+                "left": 394.015625, \n+                "top": 203\n+            }, \n+            "post_job_actions": {\n+                "HideDatasetActiontext_file": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "text_file"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63", \n+            "tool_state": "{\\"__page__\\": 0, \\"contaminants\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"limits\\": \\"null\\", \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.63", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "ece63296-d0de-4fa6-9eb0-a3539cc8d2ea"\n+        }, \n+        "3": {\n+            "annotation": "", \n+            "id": 3, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "FASTQ Groomer", \n+            "outputs": [\n+                {\n+                    "name": "output_file", \n+                    "type": "fastqsanger"\n+                }\n+            ], \n+            "position": {\n+                "left": 499.484375, \n+                "top": 474.890625\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu'..b' "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_unaligned_reads_l"\n+                }, \n+                "HideDatasetActionoutput_unaligned_reads_r": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "output_unaligned_reads_r"\n+                }\n+            }, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"library\\": \\"{\\\\\\"aligned_file\\\\\\": \\\\\\"False\\\\\\", \\\\\\"unaligned_file\\\\\\": \\\\\\"False\\\\\\", \\\\\\"input_2\\\\\\": null, \\\\\\"__current_case__\\\\\\": 1, \\\\\\"input_1\\\\\\": null, \\\\\\"type\\\\\\": \\\\\\"paired\\\\\\", \\\\\\"paired_options\\\\\\": {\\\\\\"paired_options_selector\\\\\\": \\\\\\"no\\\\\\", \\\\\\"__current_case__\\\\\\": 1}}\\", \\"reference_genome\\": \\"{\\\\\\"source\\\\\\": \\\\\\"indexed\\\\\\", \\\\\\"__current_case__\\\\\\": 0, \\\\\\"index\\\\\\": \\\\\\"IGC\\\\\\"}\\", \\"rg\\": \\"{\\\\\\"rg_selector\\\\\\": \\\\\\"do_not_set\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"save_mapping_stats\\": \\"\\\\\\"False\\\\\\"\\", \\"analysis_type\\": \\"{\\\\\\"analysis_type_selector\\\\\\": \\\\\\"simple\\\\\\", \\\\\\"presets\\\\\\": \\\\\\"--very-sensitive-local\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+            "tool_version": "2.2.6.2", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "80b3aa7d-c494-4a6d-9ec0-028641fc477e"\n+        }, \n+        "11": {\n+            "annotation": "", \n+            "id": 11, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 10, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Create GeneList Outputs", \n+            "outputs": [\n+                {\n+                    "name": "gene", \n+                    "type": "txt"\n+                }, \n+                {\n+                    "name": "kegg", \n+                    "type": "kegg"\n+                }, \n+                {\n+                    "name": "list", \n+                    "type": "list"\n+                }, \n+                {\n+                    "name": "anno_txt", \n+                    "type": "txt"\n+                }\n+            ], \n+            "position": {\n+                "left": 2040.953125, \n+                "top": 651.765625\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "geneList", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.63", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "a6796f6d-0028-45db-9f68-057601c48156"\n+        }, \n+        "12": {\n+            "annotation": "", \n+            "id": 12, \n+            "input_connections": {\n+                "input_file": {\n+                    "id": 11, \n+                    "output_name": "gene"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Count Keggs", \n+            "outputs": [\n+                {\n+                    "name": "kegg_count", \n+                    "type": "txt"\n+                }\n+            ], \n+            "position": {\n+                "left": 2395.953125, \n+                "top": 555.765625\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "countKeggs", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input_file\\": \\"null\\"}", \n+            "tool_version": "0.63", \n+            "type": "tool", \n+            "user_outputs": [], \n+            "uuid": "dceeae01-8956-479e-927c-4972a907bc9f"\n+        }\n+    }, \n+    "uuid": "5378670e-9e06-4b0c-93df-f6cbd41f646a"\n+}\n\\ No newline at end of file\n'