# HG changeset patch
# User marcel
# Date 1326990785 18000
# Node ID e047a2629ecf8536092196ecee8c95befe490800
# Parent  b17805005cc8021ccb53d79b199a80baf0fe73e3
Uploaded

diff -r b17805005cc8 -r e047a2629ecf Docking-preparation.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Docking-preparation.ga	Thu Jan 19 11:33:05 2012 -0500
@@ -0,0 +1,273 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "Water finding, contraints generation, pocket detection and grid building", 
+    "format-version": "0.1", 
+    "name": "Docking-preparation: constraints, water, pocket-detection", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Receptor"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 251.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Receptor\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "pdb-file w/ water molecules"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 198, 
+                "top": 325
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"pdb-file w/ water molecules\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference ligand"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 254.5, 
+                "top": 491
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference ligand\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "i": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ProteinProtonator", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "pdb"
+                }
+            ], 
+            "position": {
+                "left": 388.5, 
+                "top": 255
+            }, 
+            "tool_errors": null, 
+            "tool_id": "proteinprotonator", 
+            "tool_state": "{\"i\": \"null\", \"input\": \"null\", \"ph\": \"\\\"7.0\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "rec": {
+                    "id": 3, 
+                    "output_name": "o"
+                }, 
+                "rl": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "wat": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "WaterFinder", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "pdb"
+                }
+            ], 
+            "position": {
+                "left": 600, 
+                "top": 212
+            }, 
+            "tool_errors": null, 
+            "tool_id": "waterfinder", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ai\": \"\\\"False\\\"\", \"ini\": \"null\", \"water_pdb\": \"null\", \"rl\": \"null\", \"rec\": \"null\", \"wat\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "rec": {
+                    "id": 4, 
+                    "output_name": "o"
+                }, 
+                "rl": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ConstraintsFinder", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "ini"
+                }
+            ], 
+            "position": {
+                "left": 544.5, 
+                "top": 425
+            }, 
+            "tool_errors": null, 
+            "tool_id": "constraintsfinder", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "i": {
+                    "id": 4, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [], 
+            "name": "ProteinCheck", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 912.5, 
+                "top": 244
+            }, 
+            "tool_errors": null, 
+            "tool_id": "proteincheck", 
+            "tool_state": "{\"i\": \"null\", \"ignorebrokenchains\": \"\\\"False\\\"\", \"__page__\": 0, \"input\": \"null\", \"bc\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "ini": {
+                    "id": 5, 
+                    "output_name": "o"
+                }, 
+                "rec": {
+                    "id": 4, 
+                    "output_name": "o"
+                }, 
+                "rl": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "PocketDetector", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "ini"
+                }
+            ], 
+            "position": {
+                "left": 773, 
+                "top": 420
+            }, 
+            "tool_errors": null, 
+            "tool_id": "pocketdetector", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "ini": {
+                    "id": 7, 
+                    "output_name": "o"
+                }, 
+                "rec": {
+                    "id": 4, 
+                    "output_name": "o"
+                }, 
+                "rl": {
+                    "id": 2, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "GridBuilder", 
+            "outputs": [
+                {
+                    "name": "grd", 
+                    "type": "grd.gz"
+                }
+            ], 
+            "position": {
+                "left": 982.5, 
+                "top": 425
+            }, 
+            "tool_errors": null, 
+            "tool_id": "gridbuilder", 
+            "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"configfile\": \"null\", \"ini\": \"null\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r b17805005cc8 -r e047a2629ecf IMGDock,_parallelized.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMGDock,_parallelized.ga	Thu Jan 19 11:33:05 2012 -0500
@@ -0,0 +1,1012 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Parallelized IMG docking", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "compounds to be docked"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 174, 
+                "top": 636.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"compounds to be docked\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference ligand"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 788.5, 
+                "top": 222
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference ligand\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Receptor"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 828.5, 
+                "top": 316
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Receptor\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Ini-file (optional)"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 832, 
+                "top": 384
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Ini-file (optional)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ScoreGrids"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 852, 
+                "top": 474
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ScoreGrids\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "i": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Ligand3DGenerator", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 377, 
+                "top": 631
+            }, 
+            "tool_errors": null, 
+            "tool_id": "ligand3dgenerator", 
+            "tool_state": "{\"i\": \"null\", \"rm\": \"\\\"False\\\"\", \"ph\": \"\\\"7.0\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "i": {
+                    "id": 5, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [], 
+            "name": "LigCheck", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 590, 
+                "top": 635.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": "ligcheck", 
+            "tool_state": "{\"__page__\": 0, \"nc\": \"\\\"False\\\"\", \"i\": \"null\", \"ut\": \"\\\"True\\\"\", \"ef\": \"\\\"0.5\\\"\", \"rm\": \"\\\"True\\\"\", \"ri\": \"\\\"True\\\"\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "i": {
+                    "id": 6, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [], 
+            "name": "LigandFileSplitter", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o2", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o3", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o4", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o5", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o6", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o7", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o8", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o9", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o10", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o11", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o12", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o13", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o14", 
+                    "type": "mol2/sdf/drf"
+                }, 
+                {
+                    "name": "o15", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 824.5, 
+                "top": 557
+            }, 
+            "tool_errors": null, 
+            "tool_id": "ligandfilesplitter", 
+            "tool_state": "{\"i\": \"null\", \"__page__\": 0, \"no\": \"\\\"15\\\"\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1160, 
+                "top": 205
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o2"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1163, 
+                "top": 413
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o3"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1166, 
+                "top": 604
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o4"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1167, 
+                "top": 796
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o6"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1416, 
+                "top": 210
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o7"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1415, 
+                "top": 415
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o5"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1169, 
+                "top": 989
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o8"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1416, 
+                "top": 605
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o9"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1415, 
+                "top": 797
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o11"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1688, 
+                "top": 227
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "18": {
+            "annotation": "", 
+            "id": 18, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o10"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1414, 
+                "top": 991
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "19": {
+            "annotation": "", 
+            "id": 19, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o12"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1690, 
+                "top": 419
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "20": {
+            "annotation": "", 
+            "id": 20, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o13"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1690, 
+                "top": 610
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "21": {
+            "annotation": "", 
+            "id": 21, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o14"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1688, 
+                "top": 800
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "22": {
+            "annotation": "", 
+            "id": 22, 
+            "input_connections": {
+                "grd": {
+                    "id": 4, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 7, 
+                    "output_name": "o15"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1686, 
+                "top": 993
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "23": {
+            "annotation": "", 
+            "id": 23, 
+            "input_connections": {
+                "series_i_0|i": {
+                    "id": 8, 
+                    "output_name": "o"
+                }, 
+                "series_i_10|i": {
+                    "id": 17, 
+                    "output_name": "o"
+                }, 
+                "series_i_11|i": {
+                    "id": 19, 
+                    "output_name": "o"
+                }, 
+                "series_i_12|i": {
+                    "id": 20, 
+                    "output_name": "o"
+                }, 
+                "series_i_13|i": {
+                    "id": 21, 
+                    "output_name": "o"
+                }, 
+                "series_i_14|i": {
+                    "id": 22, 
+                    "output_name": "o"
+                }, 
+                "series_i_1|i": {
+                    "id": 9, 
+                    "output_name": "o"
+                }, 
+                "series_i_2|i": {
+                    "id": 10, 
+                    "output_name": "o"
+                }, 
+                "series_i_3|i": {
+                    "id": 11, 
+                    "output_name": "o"
+                }, 
+                "series_i_4|i": {
+                    "id": 14, 
+                    "output_name": "o"
+                }, 
+                "series_i_5|i": {
+                    "id": 12, 
+                    "output_name": "o"
+                }, 
+                "series_i_6|i": {
+                    "id": 13, 
+                    "output_name": "o"
+                }, 
+                "series_i_7|i": {
+                    "id": 15, 
+                    "output_name": "o"
+                }, 
+                "series_i_8|i": {
+                    "id": 16, 
+                    "output_name": "o"
+                }, 
+                "series_i_9|i": {
+                    "id": 18, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool DockResultMerger", 
+                    "name": "k"
+                }
+            ], 
+            "name": "DockResultMerger", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 2025.5, 
+                "top": 392
+            }, 
+            "tool_errors": null, 
+            "tool_id": "dockresultmerger", 
+            "tool_state": "{\"__page__\": 0, \"min\": \"\\\"\\\"\", \"max\": \"\\\"\\\"\", \"k\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"score\": \"\\\"score\\\"\", \"series_i\": \"[{\\\"i\\\": null, \\\"__index__\\\": 0}, {\\\"i\\\": null, \\\"__index__\\\": 1}, {\\\"i\\\": null, \\\"__index__\\\": 2}, {\\\"i\\\": null, \\\"__index__\\\": 3}, {\\\"i\\\": null, \\\"__index__\\\": 4}, {\\\"i\\\": null, \\\"__index__\\\": 5}, {\\\"i\\\": null, \\\"__index__\\\": 6}, {\\\"i\\\": null, \\\"__index__\\\": 7}, {\\\"i\\\": null, \\\"__index__\\\": 8}, {\\\"i\\\": null, \\\"__index__\\\": 9}, {\\\"i\\\": null, \\\"__index__\\\": 10}, {\\\"i\\\": null, \\\"__index__\\\": 11}, {\\\"i\\\": null, \\\"__index__\\\": 12}, {\\\"i\\\": null, \\\"__index__\\\": 13}, {\\\"i\\\": null, \\\"__index__\\\": 14}]\", \"rm\": \"\\\"True\\\"\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r b17805005cc8 -r e047a2629ecf IMGDock,_unparallelized.ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IMGDock,_unparallelized.ga	Thu Jan 19 11:33:05 2012 -0500
@@ -0,0 +1,223 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "IMGDock, unparallelized", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Receptor"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 132
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Receptor\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Reference ligand"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 204, 
+                "top": 209
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Reference ligand\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "ScoreGrid file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 204, 
+                "top": 296
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"ScoreGrid file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Configuration file (optional)"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 203, 
+                "top": 383
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Configuration file (optional)\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [], 
+            "name": "Ligand3DGenerator", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 413.5, 
+                "top": 373
+            }, 
+            "tool_errors": null, 
+            "tool_id": "ligand3dgenerator", 
+            "tool_state": "{\"i\": \"null\", \"rm\": \"\\\"False\\\"\", \"ph\": \"\\\"7.0\\\"\", \"__page__\": 0}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "i": {
+                    "id": 4, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [], 
+            "name": "LigCheck", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 654, 
+                "top": 370
+            }, 
+            "tool_errors": null, 
+            "tool_id": "ligcheck", 
+            "tool_state": "{\"__page__\": 0, \"nc\": \"\\\"False\\\"\", \"i\": \"null\", \"ut\": \"\\\"True\\\"\", \"ef\": \"\\\"0.5\\\"\", \"rm\": \"\\\"True\\\"\", \"ri\": \"\\\"True\\\"\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "grd": {
+                    "id": 2, 
+                    "output_name": "output"
+                }, 
+                "i": {
+                    "id": 5, 
+                    "output_name": "o"
+                }, 
+                "ini": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "rec": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "rl": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "IMGDock", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 871, 
+                "top": 368
+            }, 
+            "tool_errors": null, 
+            "tool_id": "imeedydock", 
+            "tool_state": "{\"__page__\": 0, \"i\": \"null\", \"grd\": \"null\", \"ini\": \"null\", \"rm\": \"\\\"True\\\"\", \"rl\": \"null\", \"rec\": \"null\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "series_i_0|i": {
+                    "id": 6, 
+                    "output_name": "o"
+                }
+            }, 
+            "inputs": [], 
+            "name": "DockResultMerger", 
+            "outputs": [
+                {
+                    "name": "o", 
+                    "type": "mol2/sdf/drf"
+                }
+            ], 
+            "position": {
+                "left": 1095.5, 
+                "top": 431
+            }, 
+            "tool_errors": null, 
+            "tool_id": "dockresultmerger", 
+            "tool_state": "{\"__page__\": 0, \"min\": \"\\\"\\\"\", \"max\": \"\\\"\\\"\", \"k\": \"\\\"\\\"\", \"score\": \"\\\"score\\\"\", \"series_i\": \"[{\\\"i\\\": null, \\\"__index__\\\": 0}]\", \"rm\": \"\\\"False\\\"\"}", 
+            "tool_version": "1.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file