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view Galaxy-Workflow-Metavisitor__Workflow_for_proteic_vir2_generation_and_test.ga @ 0:c375489bbcb0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows/metavisitor_2_workflows commit ecf95caa7d5e9ab001a75cbf5fb306e7ecd3def3
author artbio
date Sun, 21 Jul 2019 19:22:52 -0400
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{
    "a_galaxy_workflow": "true", 
    "uuid": "7dbf8006-41e0-4c27-8128-68a26d02eb2d", 
    "tags": [], 
    "format-version": "0.1", 
    "version": 0, 
    "steps": {
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                {
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            "post_job_actions": {}, 
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            "label": "Get new sequences", 
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            "name": "Retrieve FASTA from NCBI"
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                {
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                {
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            "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/2.3.0", 
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            "inputs": [], 
            "position": {
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            "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"txid10239[Organism] NOT txid131567[Organism] NOT phage[All Fields] NOT patent[All Fields] NOT chimeric[Title] NOT vector[Title] NOT method[Title] NOT X174[All Fields] AND 30:9000[Sequence length] NOT 2017/09:2075[PDAT]\\\"\", \"dbname\": \"\\\"protein\\\"\", \"dry_run\": \"\\\"false\\\"\"}", 
            "label": "Get old sequences", 
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            "id": 0, 
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            "uuid": "f10e16ec-5da8-460a-a1df-5a8a7c1e9e81", 
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            "outputs": [
                {
                    "type": "tabular", 
                    "name": "output1"
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            "post_job_actions": {}, 
            "workflow_outputs": [
                {
                    "output_name": "output1", 
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            }, 
            "inputs": [
                {
                    "name": "db_opts", 
                    "description": "runtime parameter for tool NCBI BLAST+ blastn"
                }, 
                {
                    "name": "query", 
                    "description": "runtime parameter for tool NCBI BLAST+ blastn"
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            ], 
            "position": {
                "top": 607, 
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            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"__current_case__\\\": 2, \\\"ext_cols\\\": [\\\"slen\\\"], \\\"ids_cols\\\": null, \\\"misc_cols\\\": null, \\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"tax_cols\\\": null}\", \"adv_opts\": \"{\\\"__current_case__\\\": 0, \\\"adv_opts_selector\\\": \\\"basic\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\", \\\"db_opts_selector\\\": \\\"histdb\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"subject\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
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                "HideDatasetActionoutfile": {
                    "output_name": "outfile", 
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            "workflow_outputs": [], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1", 
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                    "id": 0
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            "inputs": [
                {
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                {
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                    "description": "runtime parameter for tool NCBI BLAST+ makeblastdb"
                }
            ], 
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            "label": "vir2 blastdb", 
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            }, 
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            "errors": null, 
            "uuid": "0f9a007f-a745-4c95-b2d0-4f1ee836d8b1", 
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            "outputs": [
                {
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                    "name": "output_file"
                }
            ], 
            "post_job_actions": {
                "RenameDatasetActionoutput_file": {
                    "output_name": "output_file", 
                    "action_type": "RenameDatasetAction", 
                    "action_arguments": {
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                    }
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            "workflow_outputs": [
                {
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                    "uuid": "b5e71e9d-ef3b-4a33-a40c-1a5b00062e86", 
                    "label": null
                }
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            }, 
            "inputs": [
                {
                    "name": "blast_file", 
                    "description": "runtime parameter for tool Blast Unmatched"
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                {
                    "name": "fasta_file", 
                    "description": "runtime parameter for tool Blast Unmatched"
                }
            ], 
            "position": {
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            "tool_state": "{\"blast_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fasta_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
            "label": "Get non matched sequences", 
            "type": "tool", 
            "id": 4, 
            "tool_shed_repository": {
                "owner": "artbio", 
                "changeset_revision": "fffdb903f2d1", 
                "name": "blast_unmatched", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Blast Unmatched"
        }
    }, 
    "annotation": "", 
    "name": "Metavisitor: Workflow for proteic vir2 generation and test"
}