comparison blockclust_workflow_clustering.ga @ 12:62212df99efd draft

blockclust workflows 1.1.0

11:1e6d0af8c450

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    "annotation": "Until clustering step. No post processing included.", 
    "format-version": "0.1", 
    "name": "BlockClustWorkflow_clustering", 
    "steps": {
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            "id": 0, 
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                {
                    "description": "", 
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                "top": 334.5
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                    "name": "tags_bed", 
                    "type": "bed"

                    "name": "cluster_hclust", 
                    "type": "pdf"
                }
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            "position": {
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                "top": 291.5
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                {
                    "name": "out_file1", 
                    "type": "input"
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                "top": 323
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                    "output_name": "out_file1"
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            }, 
            "inputs": [], 
            "name": "blockbuster", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "tabular"
                }
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            "position": {
                "left": 961.5, 
                "top": 271.5
            }, 
            "post_job_actions": {
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                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
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            "tool_errors": null, 
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            "tool_version": "0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "4": {
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            "id": 4, 
            "input_connections": {
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            }, 
            "inputs": [
                {

                {
                    "description": "runtime parameter for tool BlockClust", 
                    "name": "tool_mode"
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            "name": "BlockClust", 
            "outputs": [
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                    "name": "tags_bed", 
                    "type": "bed"

                    "name": "cluster_hclust", 
                    "type": "pdf"
                }
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            "position": {
                "left": 1268.5, 
                "top": 305.5
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                    "action_type": "HideDatasetAction", 

                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "tags_bed"
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            "tool_errors": null, 
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            "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", 
            "type": "tool", 
            "user_outputs": []
        }
    }
}

12:62212df99efd

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "blockclust 1.1.0 clustering", 
    "steps": {
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            "annotation": "", 
            "content_id": null, 
            "errors": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [], 
            "label": "blockclust_input", 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 212
            }, 
            "tool_id": null, 
            "tool_state": "{}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "b6e23dd8-46ca-4bd6-87f3-2f6b741b459b", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "d8c12432-a0db-4cba-a815-aba6a2de9626"
                }
            ]
        }, 
        "1": {
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            "errors": null, 
            "id": 1, 
            "input_connections": {
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                    "output_name": "output"
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            }, 
            "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": {
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                }
            }, 
            "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": []
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        "2": {
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            "errors": null, 
            "id": 2, 
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                    "id": 1, 
                    "output_name": "output1"
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            }, 
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                {
                    "description": "runtime parameter for tool BlockClust", 
                    "name": "tool_mode"
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            ], 
            "label": null, 
            "name": "BlockClust", 
            "outputs": [
                {
                    "name": "tags_bed", 
                    "type": "bed"

                    "name": "cluster_hclust", 
                    "type": "pdf"
                }
            ], 
            "position": {
                "left": 788, 
                "top": 212
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                    "output_name": "sim_tab_out"
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            "tool_shed_repository": {
                "changeset_revision": "aab6cf87b40a", 
                "name": "blockclust", 
                "owner": "rnateam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
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            "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": [
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                    "label": "tags_bed", 
                    "output_name": "tags_bed", 
                    "uuid": "39f8722a-8444-42f8-8104-f81201804c9c"
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        "3": {
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            "inputs": [
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                    "description": "runtime parameter for tool Sort", 
                    "name": "infile"
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            "label": null, 
            "name": "Sort", 
            "outputs": [
                {
                    "name": "outfile", 
                    "type": "input"
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                "top": 212
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                    "action_type": "HideDatasetAction", 
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                    "output_name": "clusters", 
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                    "output_name": "hclust_plot", 
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    "tags": [], 
    "uuid": "4cecbf1c-0535-4c04-857a-550a9e0a3ede"
}