Repository 'chipseq_workflows'
hg clone https://toolshed.g2.bx.psu.edu/repos/stemcellcommons/chipseq_workflows

Changeset 9:4b0ceb4c5971 (2019-01-14)
Previous changeset 8:358360fdeea9 (2017-10-24) Next changeset 10:b1a24c47ff63 (2019-01-15)
Commit message:
Add mm9 version
added:
ChIP-seq_Peak_Calling_-_Mouse_(mm9).ga
b
diff -r 358360fdeea9 -r 4b0ceb4c5971 ChIP-seq_Peak_Calling_-_Mouse_(mm9).ga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/ChIP-seq_Peak_Calling_-_Mouse_(mm9).ga Mon Jan 14 14:44:15 2019 -0500
[
b'@@ -0,0 +1,597 @@\n+{\n+    "a_galaxy_workflow": "true", \n+     "annotation": "{\\n\\t\\"description\\": \\"Identify enriched regions (peaks) in ChIP-seq data. Reads are aligned to the mouse (mm9) reference genome.\\",\\n\\t\\"file_relationship\\": {\\n\\t\\t\\"value_type\\": \\"LIST\\",\\n\\t\\t\\"name\\": \\"List of FASTQ Pairs\\",\\n\\t\\t\\"file_relationship\\": {\\n\\t\\t\\t\\"file_relationship\\": {},\\n\\t\\t\\t\\"value_type\\": \\"PAIR\\",\\n\\t\\t\\t\\"name\\": \\"Paired FASTQ files\\",\\n\\t\\t\\t\\"input_files\\": [{\\n\\t\\t\\t\\t\\t\\"allowed_filetypes\\": [{\\n\\t\\t\\t\\t\\t\\t\\"name\\": \\"FASTQ\\"\\n\\t\\t\\t\\t\\t}],\\n\\t\\t\\t\\t\\t\\"name\\": \\"Treatment FASTQ\\",\\n\\t\\t\\t\\t\\t\\"description\\": \\"Treatment FASTQ\\"\\n\\t\\t\\t\\t},\\n\\t\\t\\t\\t{\\n\\t\\t\\t\\t\\t\\"allowed_filetypes\\": [{\\n\\t\\t\\t\\t\\t\\t\\"name\\": \\"FASTQ\\"\\n\\t\\t\\t\\t\\t}],\\n\\t\\t\\t\\t\\t\\"name\\": \\"Control FASTQ\\",\\n\\t\\t\\t\\t\\t\\"description\\": \\"Control FASTQ\\"\\n\\t\\t\\t\\t}\\n\\t\\t\\t]\\n\\t\\t}\\n\\t}\\n}", \n+    "format-version": "0.1", \n+    "name": "ChIP-seq Peak Calling - Mouse (mm9)", \n+    "steps": {\n+        "0": {\n+            "annotation": "", \n+            "content_id": null, \n+            "id": 0, \n+            "input_connections": {}, \n+            "inputs": [\n+                {\n+                    "description": "", \n+                    "name": "Input Dataset Collection"\n+                }\n+            ], \n+            "label": null, \n+            "name": "Input dataset collection", \n+            "outputs": [], \n+            "position": {\n+                "left": 200, \n+                "top": 395.5\n+            }, \n+            "tool_errors": null, \n+            "tool_id": null, \n+            "tool_state": "{\\"collection_type\\": \\"paired\\", \\"name\\": \\"Input Dataset Collection\\"}", \n+            "tool_version": null, \n+            "type": "data_collection_input", \n+            "uuid": "356ec3d6-e4d4-442c-bbd6-84acab454f1a", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output", \n+                    "uuid": "f6218906-b7d9-45d0-8d2a-1eb96c3e9a8e"\n+                }\n+            ]\n+        }, \n+        "1": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/refinery-platform/split_paired_collection/split_paired_collection/0.2", \n+            "id": 1, \n+            "input_connections": {\n+                "input_collection": {\n+                    "id": 0, \n+                    "output_name": "output"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Split Paired Collection", \n+            "outputs": [\n+                {\n+                    "name": "forward_element", \n+                    "type": "data"\n+                }, \n+                {\n+                    "name": "reverse_element", \n+                    "type": "data"\n+                }\n+            ], \n+            "position": {\n+                "left": 474.5, \n+                "top": 376.5\n+            }, \n+            "post_job_actions": {\n+                "ChangeDatatypeActionforward_element": {\n+                    "action_arguments": {\n+                        "newtype": "fastqsanger"\n+                    }, \n+                    "action_type": "ChangeDatatypeAction", \n+                    "output_name": "forward_element"\n+                }, \n+                "ChangeDatatypeActionreverse_element": {\n+                    "action_arguments": {\n+                        "newtype": "fastqsanger"\n+                    }, \n+                    "action_type": "ChangeDatatypeAction", \n+                    "output_name": "reverse_element"\n+                }, \n+                "HideDatasetActionforward_element": {\n+                    "action_arguments": {}, \n+                    "action_type": "HideDatasetAction", \n+                    "output_name": "forward_element"\n+                }, \n+                "HideDatasetActionreverse_element": {\n+                    "action_arguments": {}, \n+                    "action'..b' \\\\\\"qvalue\\\\\\": \\\\\\"0.05\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"advanced_options\\": \\"{\\\\\\"advanced_options_selector\\\\\\": \\\\\\"off\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"input_treatment_file\\": \\"null\\", \\"nomodel_type\\": \\"{\\\\\\"nomodel_type_selector\\\\\\": \\\\\\"create_model\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"band_width\\": \\"\\\\\\"300\\\\\\"\\"}", \n+            "tool_version": "2.1.0.20151222.0", \n+            "type": "tool", \n+            "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "output_plot", \n+                    "uuid": "456fea9e-c16f-4baa-af2f-e22a65cc6b7f"\n+                }\n+            ]\n+        }, \n+        "9": {\n+            "annotation": "", \n+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", \n+            "id": 9, \n+            "input_connections": {\n+                "infile_control": {\n+                    "id": 8, \n+                    "output_name": "output_control_lambda"\n+                }, \n+                "infile_treatment": {\n+                    "id": 8, \n+                    "output_name": "output_treat_pileup"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "MACS2 bdgcmp", \n+            "outputs": [\n+                {\n+                    "name": "outfile", \n+                    "type": "bedgraph"\n+                }\n+            ], \n+            "position": {\n+                "left": 2001.5, \n+                "top": 427.5\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"infile_control\\": \\"null\\", \\"bdgcmp_options\\": \\"{\\\\\\"bdgcmp_options_selector\\\\\\": \\\\\\"ppois\\\\\\", \\\\\\"__current_case__\\\\\\": 3}\\", \\"infile_treatment\\": \\"null\\"}", \n+            "tool_version": "2.1.0.20151222.0", \n+            "type": "tool", \n+            "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "outfile", \n+                    "uuid": "9b313409-0812-495c-848b-aaab5eaf05b4"\n+                }\n+            ]\n+        }, \n+        "10": {\n+            "annotation": "{\\"out_file1\\": {\\"name\\": \\"MACS2_bigwig\\", \\"description\\": \\"\\", \\"type\\": \\"bigwig\\"}}", \n+            "content_id": "wig_to_bigWig", \n+            "id": 10, \n+            "input_connections": {\n+                "input1": {\n+                    "id": 9, \n+                    "output_name": "outfile"\n+                }\n+            }, \n+            "inputs": [], \n+            "label": null, \n+            "name": "Wig/BedGraph-to-bigWig", \n+            "outputs": [\n+                {\n+                    "name": "out_file1", \n+                    "type": "bigwig"\n+                }\n+            ], \n+            "position": {\n+                "left": 2243.546875, \n+                "top": 432.71875\n+            }, \n+            "post_job_actions": {}, \n+            "tool_errors": null, \n+            "tool_id": "wig_to_bigWig", \n+            "tool_state": "{\\"__page__\\": 0, \\"__rerun_remap_job_id__\\": null, \\"input1\\": \\"null\\", \\"settings\\": \\"{\\\\\\"settingsType\\\\\\": \\\\\\"preset\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\"}", \n+            "tool_version": "1.1.0", \n+            "type": "tool", \n+            "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", \n+            "workflow_outputs": [\n+                {\n+                    "label": null, \n+                    "output_name": "out_file1", \n+                    "uuid": "5bbfca2d-617f-43d8-8eb9-a4d6a9a07eb8"\n+                }\n+            ]\n+        }\n+    }, \n+    "uuid": "99c95324-e964-41d7-90fe-7c70d06942cf"\n+}\n\\ No newline at end of file\n'