Mercurial > repos > rnateam > blockclust_workflow
view blockclust_workflow_clustering.ga @ 3:a1c846233094 draft
Uploaded
author | rnateam |
---|---|
date | Wed, 09 Jul 2014 07:49:36 -0400 |
parents | 25afbac62e0d |
children | 59e321cafca7 |
line wrap: on
line source
{ "a_galaxy_workflow": "true", "annotation": "Until clustering step. No post processing included.", "format-version": "0.1", "name": "BlockClustWorkflow_clustering", "steps": { "0": { "annotation": "", "id": 0, "input_connections": {}, "inputs": [ { "description": "", "name": "Input BAM file" } ], "name": "Input dataset", "outputs": [], "position": { "left": 217, "top": 282.5 }, "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": [ { "name": "tags_bed", "type": "bed" }, { "name": "hclust_plot", "type": "pdf" }, { "name": "clusters", "type": "bed" }, { "name": "model_based_pred_bed", "type": "bed" }, { "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": 446.5, "top": 239.5 }, "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": "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": [], "name": "Sort", "outputs": [ { "name": "out_file1", "type": "input" } ], "position": { "left": 740, "top": 271 }, "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\\\"}]\"}", "tool_version": "1.0.3", "type": "tool", "user_outputs": [] }, "3": { "annotation": "", "id": 3, "input_connections": { "input": { "id": 2, "output_name": "out_file1" } }, "inputs": [], "name": "blockbuster", "outputs": [ { "name": "output", "type": "tabular" } ], "position": { "left": 961.5, "top": 219.5 }, "post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" } }, "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", "type": "tool", "user_outputs": [] }, "4": { "annotation": "", "id": 4, "input_connections": { "tool_mode|input_bbo": { "id": 3, "output_name": "output" } }, "inputs": [ { "description": "runtime parameter for tool BlockClust", "name": "tool_mode" } ], "name": "BlockClust", "outputs": [ { "name": "tags_bed", "type": "bed" }, { "name": "hclust_plot", "type": "pdf" }, { "name": "clusters", "type": "bed" }, { "name": "model_based_pred_bed", "type": "bed" }, { "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": 1220.5, "top": 375.5 }, "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" }, "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": "toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0", "tool_state": "{\"tool_mode\": \"{\\\"pred\\\": {\\\"pred_mode\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"enable_pred\\\": \\\"yes\\\", \\\"__current_case__\\\": 0}, \\\"operation\\\": \\\"clust\\\", \\\"reference\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"input_bbo\\\": null}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.0", "type": "tool", "user_outputs": [] } } }