# HG changeset patch
# User rnateam
# Date 1544456836 18000
# Node ID f320021d07e1fa797fc556966bf77150f97b340e
# Parent  62212df99efd1194c85a1a57954b24ca6c340ea9
Uploaded

diff -r 62212df99efd -r f320021d07e1 blockclust_workflow_complete.ga
--- a/blockclust_workflow_complete.ga	Mon Dec 10 10:46:54 2018 -0500
+++ b/blockclust_workflow_complete.ga	Mon Dec 10 10:47:16 2018 -0500
@@ -2,41 +2,102 @@
     "a_galaxy_workflow": "true", 
     "annotation": "", 
     "format-version": "0.1", 
-    "name": "BlockClustWorkflow_complete", 
+    "name": "blockclust 1.1.0 complete", 
     "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": 240, 
-                "top": 380.5
+                "left": 200, 
+                "top": 338
             }, 
-            "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": 338
+            }, 
+            "post_job_actions": {}, 
+            "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": [
+                {
+                    "label": null, 
+                    "output_name": "output1", 
+                    "uuid": "22295821-a765-4e6c-804f-6c710e26923f"
+                }
+            ]
+        }, 
+        "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": {
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-                "top": 337.5
+                "left": 788, 
+                "top": 338
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             "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": {
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                     "output_name": "tags_bed"
                 }
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", 
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-            "type": "tool", 
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-            "id": 2, 
-            "input_connections": {
-                "input": {
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-                    "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": 763, 
-                "top": 369
+                "left": 1116, 
+                "top": 338
             }, 
             "post_job_actions": {
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                     "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
+                    "output_name": "outfile"
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-            "tool_id": "sort1", 
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-            "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": {
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+                "name": "text_processing", 
+                "owner": "bgruening", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2", 
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+                    "output_name": "outfile"
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-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool blockbuster", 
+                    "name": "input"
+                }
+            ], 
+            "label": null, 
             "name": "blockbuster", 
             "outputs": [
                 {
                     "name": "output", 
-                    "type": "tabular"
+                    "type": "bed"
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+                "left": 1376, 
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-                    "action_type": "HideDatasetAction", 
-                    "output_name": "output"
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+            "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"
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-            "tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1", 
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-            "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"
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-        "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": {
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                     "output_name": "output"
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@@ -214,6 +312,7 @@
                     "name": "tool_mode"
                 }
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+            "label": null, 
             "name": "BlockClust", 
             "outputs": [
                 {
@@ -250,8 +349,8 @@
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-                "top": 359.5
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             "post_job_actions": {
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@@ -275,64 +374,116 @@
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-            "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", 
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             "type": "tool", 
-            "user_outputs": []
+            "uuid": "e41a16eb-4edd-4f9e-b615-44d0c2988b63", 
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+                    "output_name": "clusters", 
+                    "uuid": "287b4bae-55a1-4f38-b1c3-62ae60b4d950"
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+                    "output_name": "hclust_plot", 
+                    "uuid": "01744525-c294-4534-814d-547e87f7cc49"
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                     "output_name": "clusters"
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+                    "description": "runtime parameter for tool Extract Genomic DNA", 
+                    "name": "interpret_features"
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+                    "description": "runtime parameter for tool Extract Genomic DNA", 
+                    "name": "input"
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+                    "description": "runtime parameter for tool Extract Genomic DNA", 
+                    "name": "reference_genome_cond"
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             "name": "Extract Genomic DNA", 
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                 {
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                     "type": "input"
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-            "name": "Search covariance model(s)", 
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                     "name": "outfile", 
@@ -344,8 +495,8 @@
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@@ -359,31 +510,53 @@
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+            "tool_version": "1.1.2.0", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "842f09a0-b91c-4a9b-a3a5-019f0fda1aba", 
+            "workflow_outputs": []
         }, 
-        "7": {
+        "8": {
             "annotation": "", 
-            "id": 7, 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0", 
+            "errors": null, 
+            "id": 8, 
             "input_connections": {
                 "tool_mode|clusters_bed": {
-                    "id": 4, 
+                    "id": 5, 
                     "output_name": "clusters"
                 }, 
                 "tool_mode|cmsearch_out": {
-                    "id": 6, 
+                    "id": 7, 
                     "output_name": "outfile"
                 }, 
                 "tool_mode|sim_tab_in": {
-                    "id": 4, 
+                    "id": 5, 
                     "output_name": "sim_tab_out"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "tool_mode"
+                }, 
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "tool_mode"
+                }, 
+                {
+                    "description": "runtime parameter for tool BlockClust", 
+                    "name": "tool_mode"
+                }
+            ], 
+            "label": null, 
             "name": "BlockClust", 
             "outputs": [
                 {
@@ -420,8 +593,8 @@
                 }
             ], 
             "position": {
-                "left": 2184.5, 
-                "top": 403.5
+                "left": 2639, 
+                "top": 338
             }, 
             "post_job_actions": {
                 "HideDatasetActionclusters": {
@@ -455,12 +628,31 @@
                     "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\": \"{\\\"cmsearch_out\\\": null, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": null, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": null}\", \"__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\": \"{\\\"cmsearch_out\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"operation\\\": \\\"post\\\", \\\"clusters_bed\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2, \\\"sim_tab_in\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
+            "tool_version": "1.1.0", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "dfdaf591-1d6f-45f0-bf05-4fac5680155e", 
+            "workflow_outputs": [
+                {
+                    "label": null, 
+                    "output_name": "cluster_hclust", 
+                    "uuid": "75860090-3020-4281-9887-b73389b9c207"
+                }, 
+                {
+                    "label": null, 
+                    "output_name": "cluster_dist", 
+                    "uuid": "c749ddcc-628b-4e46-a61d-dfbe00901964"
+                }
+            ]
         }
-    }
+    }, 
+    "tags": [], 
+    "uuid": "a60be50d-44e1-4fb5-90a0-3b849ceaf3e3"
 }
\ No newline at end of file