# HG changeset patch
# User yutaka-saito
# Date 1429456911 14400
# Node ID 5a5d062e3b330837f1df3e4a181b21ba648227e3

Uploaded

diff -r 000000000000 -r 5a5d062e3b33 Galaxy-Workflow-bisulfighter.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-bisulfighter.ga	Sun Apr 19 11:21:51 2015 -0400
@@ -0,0 +1,178 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "bisulfighter", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "single-end fastq reads for sample1"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"single-end fastq reads for sample1\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "e06f739a-dceb-4277-adaa-421fa3c8b404"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "single-end fastq reads for sample2"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"single-end fastq reads for sample2\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "6aae6752-e196-47ec-bd17-e348c9e274cb"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "read|in": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool bsfcall", 
+                    "name": "reference"
+                }
+            ], 
+            "label": null, 
+            "name": "bsfcall", 
+            "outputs": [
+                {
+                    "name": "outres", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outlog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 435, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yutaka-saito/bsfcall/bsfcall/1.0.0", 
+            "tool_state": "{\"read\": \"{\\\"end\\\": \\\"single-end\\\", \\\"__current_case__\\\": 0, \\\"in\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "9b5f9915-d4e4-41c7-bb0b-4188579abf35"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "read|in": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool bsfcall", 
+                    "name": "reference"
+                }
+            ], 
+            "label": null, 
+            "name": "bsfcall", 
+            "outputs": [
+                {
+                    "name": "outres", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outlog", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 435, 
+                "top": 358
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yutaka-saito/bsfcall/bsfcall/1.0.0", 
+            "tool_state": "{\"read\": \"{\\\"end\\\": \\\"single-end\\\", \\\"__current_case__\\\": 0, \\\"in\\\": null}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"reference\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "04af3b7b-35a9-4bfd-a6f5-1b1c84fb1185"
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "intype|in1": {
+                    "id": 2, 
+                    "output_name": "outres"
+                }, 
+                "intype|in2": {
+                    "id": 3, 
+                    "output_name": "outres"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "ComMet", 
+            "outputs": [
+                {
+                    "name": "outdmc", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outdmr", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 763, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/yutaka-saito/commet/ComMet/1.0.0", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"intype\": \"{\\\"in2\\\": null, \\\"mapper\\\": \\\"bsf-call\\\", \\\"in1\\\": null, \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": [], 
+            "uuid": "4e503e50-4023-45e8-8738-27e0fdcce949"
+        }
+    }, 
+    "uuid": "9d6d0530-2ed9-4346-91a5-02d8464be49c"
+}
\ No newline at end of file