Mercurial > repos > rnateam > blockclust_workflow

changeset 10:d1c4bdaecd97 draft

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Uploaded
author rnateam
date Thu, 23 Jan 2014 07:08:38 -0500
parents bfc6f50279d6
children 0306182df00b
files blockclust_workflow.ga
diffstat 1 files changed, 240 insertions(+), 62 deletions(-) [+]
line wrap: on
line diff
--- a/blockclust_workflow.ga	Thu Jan 23 06:15:53 2014 -0500
+++ b/blockclust_workflow.ga	Thu Jan 23 07:08:38 2014 -0500
@@ -8,6 +8,34 @@
             "annotation": "", 
             "id": 0, 
             "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input BAM file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 267, 
+                "top": 257.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input BAM file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "tool_mode|reads_bam": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
             "inputs": [], 
             "name": "BlockClust", 
             "outputs": [
@@ -24,36 +52,85 @@
                     "type": "bed"
                 }, 
                 {
-                    "name": "sim_tab_out", 
-                    "type": "tabular"
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
                 }, 
                 {
-                    "name": "analysis", 
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
                     "type": "tabular"
                 }, 
                 {
                     "name": "cluster_dist", 
                     "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
                 }
             ], 
             "position": {
-                "left": 200, 
-                "top": 308
+                "left": 524, 
+                "top": 323
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActioncluster_dist": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_dist"
+                }, 
+                "HideDatasetActioncluster_hclust": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_hclust"
+                }, 
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionhclust_plot": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "hclust_plot"
+                }, 
+                "HideDatasetActionmodel_based_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "model_based_pred_bed"
+                }, 
+                "HideDatasetActionnearest_neighbour_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
+                }, 
+                "HideDatasetActiontags_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
+                }
+            }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__page__\": 0}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "1": {
+        "2": {
             "annotation": "", 
-            "id": 1, 
+            "id": 2, 
             "input_connections": {
                 "input": {
-                    "id": 0, 
+                    "id": 1, 
                     "output_name": "tags_bed"
                 }
             }, 
@@ -66,10 +143,16 @@
                 }
             ], 
             "position": {
-                "left": 466, 
-                "top": 308
+                "left": 797, 
+                "top": 355
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
             "tool_errors": null, 
             "tool_id": "sort1", 
             "tool_state": "{\"__page__\": 0, \"style\": \"\\\"alpha\\\"\", \"column\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"order\": \"\\\"ASC\\\"\", \"input\": \"null\", \"column_set\": \"[{\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 0, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"6\\\"}, \\\"other_style\\\": \\\"alpha\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 1, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"other_style\\\": \\\"num\\\"}, {\\\"other_order\\\": \\\"ASC\\\", \\\"__index__\\\": 2, \\\"other_column\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}, \\\"other_style\\\": \\\"num\\\"}]\"}", 
@@ -77,12 +160,12 @@
             "type": "tool", 
             "user_outputs": []
         }, 
-        "2": {
+        "3": {
             "annotation": "", 
-            "id": 2, 
+            "id": 3, 
             "input_connections": {
                 "input": {
-                    "id": 1, 
+                    "id": 2, 
                     "output_name": "out_file1"
                 }
             }, 
@@ -95,30 +178,30 @@
                 }
             ], 
             "position": {
-                "left": 694, 
-                "top": 308
+                "left": 970, 
+                "top": 225
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 
-            "tool_state": "{\"distance\": \"\\\"30\\\"\", \"scale\": \"\\\"0.4\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"1\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"2.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"10.0\\\"\"}", 
+            "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"1\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", 
             "tool_version": "0.1", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "3": {
+        "4": {
             "annotation": "", 
-            "id": 3, 
+            "id": 4, 
             "input_connections": {
-                "mode|input_bbo": {
-                    "id": 2, 
+                "tool_mode|input_bbo": {
+                    "id": 3, 
                     "output_name": "output"
                 }
             }, 
             "inputs": [
                 {
                     "description": "runtime parameter for tool BlockClust", 
-                    "name": "mode"
+                    "name": "tool_mode"
                 }
             ], 
             "name": "BlockClust", 
@@ -136,36 +219,75 @@
                     "type": "bed"
                 }, 
                 {
-                    "name": "sim_tab_out", 
-                    "type": "tabular"
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
                 }, 
                 {
-                    "name": "analysis", 
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
                     "type": "tabular"
                 }, 
                 {
                     "name": "cluster_dist", 
                     "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
                 }
             ], 
             "position": {
-                "left": 922, 
-                "top": 308
+                "left": 1232, 
+                "top": 321
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActioncluster_dist": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_dist"
+                }, 
+                "HideDatasetActioncluster_hclust": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "cluster_hclust"
+                }, 
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionnearest_neighbour_pred_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
+                }, 
+                "HideDatasetActiontags_bed": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
+                }
+            }, 
             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\"}", 
+            "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__page__\": 0}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "4": {
+        "5": {
             "annotation": "", 
-            "id": 4, 
+            "id": 5, 
             "input_connections": {
                 "input": {
-                    "id": 3, 
+                    "id": 4, 
                     "output_name": "clusters"
                 }
             }, 
@@ -178,23 +300,29 @@
                 }
             ], 
             "position": {
-                "left": 1164, 
-                "top": 201
+                "left": 1495, 
+                "top": 248
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
             "tool_errors": null, 
             "tool_id": "Extract genomic DNA 1", 
             "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"interpret_features\": \"\\\"yes\\\"\", \"__rerun_remap_job_id__\": null, \"seq_source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\"}", 
-            "tool_version": "2.2.2", 
+            "tool_version": "2.2.3", 
             "type": "tool", 
             "user_outputs": []
         }, 
-        "5": {
+        "6": {
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-            "id": 5, 
+            "id": 6, 
             "input_connections": {
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+                    "id": 5, 
                     "output_name": "out_file1"
                 }
             }, 
@@ -211,31 +339,42 @@
                 }
             ], 
             "position": {
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-                "top": 200
+                "left": 1753, 
+                "top": 247
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActionmultiple_alignment_output": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "multiple_alignment_output"
+                }, 
+                "HideDatasetActionoutfile": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outfile"
+                }
+            }, 
             "tool_errors": null, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.1", 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2", 
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-            "tool_version": "1.1.0.1", 
+            "tool_version": "1.1.0.2", 
             "type": "tool", 
             "user_outputs": []
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-        "6": {
+        "7": {
             "annotation": "", 
-            "id": 6, 
+            "id": 7, 
             "input_connections": {
-                "mode|clusters_bed": {
-                    "id": 3, 
+                "tool_mode|clusters_bed": {
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                     "output_name": "clusters"
                 }, 
-                "mode|cmsearch_out": {
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+                "tool_mode|cmsearch_out": {
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                     "output_name": "outfile"
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-                "mode|sim_tab_in": {
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+                "tool_mode|sim_tab_in": {
+                    "id": 4, 
                     "output_name": "sim_tab_out"
                 }
             }, 
@@ -255,29 +394,68 @@
                     "type": "bed"
                 }, 
                 {
-                    "name": "sim_tab_out", 
-                    "type": "tabular"
+                    "name": "model_based_pred_bed", 
+                    "type": "bed"
                 }, 
                 {
-                    "name": "analysis", 
+                    "name": "nearest_neighbour_pred_bed", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "sim_tab_out", 
                     "type": "tabular"
                 }, 
                 {
                     "name": "cluster_dist", 
                     "type": "pdf"
+                }, 
+                {
+                    "name": "cluster_hclust", 
+                    "type": "pdf"
                 }
             ], 
             "position": {
-                "left": 1738, 
-                "top": 308
+                "left": 2049, 
+                "top": 433
             }, 
-            "post_job_actions": {}, 
+            "post_job_actions": {
+                "HideDatasetActionclusters": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "clusters"
+                }, 
+                "HideDatasetActionhclust_plot": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "hclust_plot"
+                }, 
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "model_based_pred_bed"
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "nearest_neighbour_pred_bed"
+                }, 
+                "HideDatasetActionsim_tab_out": {
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "sim_tab_out"
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+                    "action_type": "HideDatasetAction", 
+                    "output_name": "tags_bed"
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             "tool_errors": null, 
             "tool_id": "testtoolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
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+            "tool_state": "{\"tool_mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__page__\": 0}", 
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             "type": "tool", 
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-}
+}
\ No newline at end of file