Mercurial > repos > rnateam > blockclust_workflow

changeset 12:62212df99efd draft

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blockclust workflows 1.1.0
author rnateam
date Mon, 10 Dec 2018 10:46:54 -0500
parents 1e6d0af8c450
children f320021d07e1
files blockclust_workflow_clustering.ga
diffstat 1 files changed, 206 insertions(+), 78 deletions(-) [+]
line wrap: on
line diff
--- a/blockclust_workflow_clustering.ga	Mon Dec 10 10:46:24 2018 -0500
+++ b/blockclust_workflow_clustering.ga	Mon Dec 10 10:46:54 2018 -0500
@@ -1,42 +1,103 @@
 {
     "a_galaxy_workflow": "true", 
-    "annotation": "Until clustering step. No post processing included.", 
+    "annotation": "", 
     "format-version": "0.1", 
-    "name": "BlockClustWorkflow_clustering", 
+    "name": "blockclust 1.1.0 clustering", 
     "steps": {
         "0": {
             "annotation": "", 
+            "content_id": null, 
+            "errors": null, 
             "id": 0, 
             "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input BAM file"
-                }
-            ], 
+            "inputs": [], 
+            "label": "blockclust_input", 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
-                "left": 217, 
-                "top": 334.5
+                "left": 200, 
+                "top": 212
             }, 
-            "tool_errors": null, 
             "tool_id": null, 
-            "tool_state": "{\"name\": \"Input BAM file\"}", 
+            "tool_state": "{}", 
             "tool_version": null, 
             "type": "data_input", 
-            "user_outputs": []
+            "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "output", 
+                    "uuid": "d8c12432-a0db-4cba-a815-aba6a2de9626"
+                }
+            ]
         }, 
         "1": {
             "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2", 
+            "errors": null, 
             "id": 1, 
             "input_connections": {
-                "tool_mode|reads_bam": {
+                "input1": {
                     "id": 0, 
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Samtools sort", 
+                    "name": "input1"
+                }
+            ], 
+            "label": null, 
+            "name": "Samtools sort", 
+            "outputs": [
+                {
+                    "name": "output1", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 460, 
+                "top": 212
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutput1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "output1"
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "f56bdb93ae58", 
+                "name": "samtools_sort", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"prim_key_cond\": \"{\\\"prim_key_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_version": "2.0.2", 
+            "type": "tool", 
+            "uuid": "327e9b59-6d4e-482e-bcdf-c7cc5d8505c9", 
+            "workflow_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", 
+            "errors": null, 
+            "id": 2, 
+            "input_connections": {
+                "tool_mode|reads_bam": {
+                    "id": 1, 
+                    "output_name": "output1"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "tool_mode"
+                }
+            ], 
+            "label": null, 
             "name": "BlockClust", 
             "outputs": [
                 {
@@ -73,8 +134,8 @@
                 }
             ], 
             "position": {
-                "left": 446.5, 
-                "top": 291.5
+                "left": 788, 
+                "top": 212
             }, 
             "post_job_actions": {
                 "HideDatasetActioncluster_dist": {
@@ -111,96 +172,133 @@
                     "action_arguments": {}, 
                     "action_type": "HideDatasetAction", 
                     "output_name": "sim_tab_out"
-                }, 
-                "HideDatasetActiontags_bed": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
+                }
+            }, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "aab6cf87b40a", 
+                "name": "blockclust", 
+                "owner": "rnateam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "uuid": "fd3043d3-609e-4303-bcb5-448cb749a319", 
+            "workflow_outputs": [
+                {
+                    "label": "tags_bed", 
+                    "output_name": "tags_bed", 
+                    "uuid": "39f8722a-8444-42f8-8104-f81201804c9c"
+                }
+            ]
+        }, 
+        "3": {
+            "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", 
+            "errors": null, 
+            "id": 3, 
+            "input_connections": {
+                "infile": {
+                    "id": 2, 
                     "output_name": "tags_bed"
                 }
             }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
-            "tool_state": "{\"tool_mode\": \"{\\\"operation\\\": \\\"pre\\\", \\\"reads_bam\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "input": {
-                    "id": 1, 
-                    "output_name": "tags_bed"
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Sort", 
+                    "name": "infile"
                 }
-            }, 
-            "inputs": [], 
+            ], 
+            "label": null, 
             "name": "Sort", 
             "outputs": [
                 {
-                    "name": "out_file1", 
+                    "name": "outfile", 
                     "type": "input"
                 }
             ], 
             "position": {
-                "left": 740, 
-                "top": 323
+                "left": 1116, 
+                "top": 212
             }, 
             "post_job_actions": {
-                "HideDatasetActionout_file1": {
+                "HideDatasetActionoutfile": {
                     "action_arguments": {}, 
                     "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
+                    "output_name": "outfile"
                 }
             }, 
-            "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\\\"}]\"}", 
-            "tool_version": "1.0.3", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1", 
+            "tool_shed_repository": {
+                "changeset_revision": "74a8bef53a00", 
+                "name": "text_processing", 
+                "owner": "bgruening", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"sortkeys\": \"[{\\\"column\\\": \\\"1\\\", \\\"__index__\\\": 0, \\\"style\\\": \\\"\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"6\\\", \\\"__index__\\\": 1, \\\"style\\\": \\\"\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"2\\\", \\\"__index__\\\": 2, \\\"style\\\": \\\"n\\\", \\\"order\\\": \\\"\\\"}, {\\\"column\\\": \\\"3\\\", \\\"__index__\\\": 3, \\\"style\\\": \\\"n\\\", \\\"order\\\": \\\"\\\"}]\", \"__page__\": null, \"ignore_case\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"header\": \"\\\"0\\\"\", \"unique\": \"\\\"false\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "1.1.1", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "ecaa7fb8-a10a-457c-9ce0-3b7f0647d1b4", 
+            "workflow_outputs": []
         }, 
-        "3": {
+        "4": {
             "annotation": "", 
-            "id": 3, 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2", 
+            "errors": null, 
+            "id": 4, 
             "input_connections": {
                 "input": {
-                    "id": 2, 
-                    "output_name": "out_file1"
+                    "id": 3, 
+                    "output_name": "outfile"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool blockbuster", 
+                    "name": "input"
+                }
+            ], 
+            "label": null, 
             "name": "blockbuster", 
             "outputs": [
                 {
                     "name": "output", 
-                    "type": "tabular"
+                    "type": "bed"
                 }
             ], 
             "position": {
-                "left": 961.5, 
-                "top": 271.5
+                "left": 1376, 
+                "top": 212
             }, 
-            "post_job_actions": {
-                "HideDatasetActionoutput": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "output"
-                }
+            "post_job_actions": {}, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "7c7ff7a3503f", 
+                "name": "blockbuster", 
+                "owner": "rnateam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 
-            "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"2\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"null\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", 
-            "tool_version": "0.1", 
+            "tool_state": "{\"distance\": \"\\\"40\\\"\", \"scale\": \"\\\"0.5\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"print\": \"\\\"bbf_reads\\\"\", \"tagFilter\": \"\\\"0\\\"\", \"merge\": \"\\\"0\\\"\", \"minBlockHeight\": \"\\\"1.0\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"minClusterHeight\": \"\\\"50.0\\\"\"}", 
+            "tool_version": "0.1.2", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "8a3db40c-ae03-49ca-b47c-559ac455d712", 
+            "workflow_outputs": [
+                {
+                    "label": "blockbuster_out", 
+                    "output_name": "output", 
+                    "uuid": "95c21ce9-e988-44b9-978e-10a27b74d18e"
+                }
+            ]
         }, 
-        "4": {
+        "5": {
             "annotation": "", 
-            "id": 4, 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", 
+            "errors": null, 
+            "id": 5, 
             "input_connections": {
                 "tool_mode|input_bbo": {
-                    "id": 3, 
+                    "id": 4, 
                     "output_name": "output"
                 }
             }, 
@@ -214,6 +312,7 @@
                     "name": "tool_mode"
                 }
             ], 
+            "label": null, 
             "name": "BlockClust", 
             "outputs": [
                 {
@@ -250,8 +349,8 @@
                 }
             ], 
             "position": {
-                "left": 1268.5, 
-                "top": 305.5
+                "left": 1694, 
+                "top": 212
             }, 
             "post_job_actions": {
                 "HideDatasetActioncluster_dist": {
@@ -275,12 +374,41 @@
                     "output_name": "tags_bed"
                 }
             }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
-            "tool_state": "{\"tool_mode\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_bbo\\\": null, \\\"pred\\\": {\\\"pred_mode\\\": \\\"model_based\\\", \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"nochr\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"operation\\\": \\\"clust\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "1.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "aab6cf87b40a", 
+                "name": "blockclust", 
+                "owner": "rnateam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"tool_mode\": \"{\\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"input_bbo\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"enable_pred\\\": \\\"yes\\\"}, \\\"nochr\\\": \\\"false\\\", \\\"__current_case__\\\": 1, \\\"operation\\\": \\\"analysis\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
+            "tool_version": "1.1.0", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "e41a16eb-4edd-4f9e-b615-44d0c2988b63", 
+            "workflow_outputs": [
+                {
+                    "label": "clusters_bed", 
+                    "output_name": "clusters", 
+                    "uuid": "287b4bae-55a1-4f38-b1c3-62ae60b4d950"
+                }, 
+                {
+                    "label": "nn_pred_bed", 
+                    "output_name": "nearest_neighbour_pred_bed", 
+                    "uuid": "6f1ae3c9-58be-4707-84e7-9936a335d743"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "hclust_plot", 
+                    "uuid": "dec50654-b78a-477d-b35e-b37269c8347d"
+                }, 
+                {
+                    "label": "model_based_pred_bed", 
+                    "output_name": "model_based_pred_bed", 
+                    "uuid": "04c1de5d-d039-4dff-9981-ba1d72e3cbca"
+                }
+            ]
         }
-    }
-}
+    }, 
+    "tags": [], 
+    "uuid": "4cecbf1c-0535-4c04-857a-550a9e0a3ede"
+}
\ No newline at end of file