view Galaxy-Workflow-Metavisitor__Trinity_test_in_Use_Case_2-2.ga @ 0:c375489bbcb0 draft

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
parents
children
line wrap: on
line source

{
    "a_galaxy_workflow": "true", 
    "uuid": "bcf798d6-3f03-40bd-acc6-74b00ce4f28b", 
    "tags": [], 
    "format-version": "0.1", 
    "version": 3, 
    "steps": {
        "1": {
            "tool_id": null, 
            "errors": null, 
            "uuid": "5561c9ef-2dbd-49e0-a11f-f023c88ed10d", 
            "tool_version": null, 
            "outputs": [], 
            "workflow_outputs": [
                {
                    "output_name": "output", 
                    "uuid": "3aba6c38-d7f8-491b-90f4-5dbbb4b89ef1", 
                    "label": null
                }
            ], 
            "annotation": "", 
            "content_id": null, 
            "input_connections": {}, 
            "inputs": [], 
            "position": {
                "top": 639.5, 
                "left": 2657
            }, 
            "tool_state": "{}", 
            "label": "Protein Blast database", 
            "type": "data_input", 
            "id": 1, 
            "name": "Input dataset"
        }, 
        "0": {
            "tool_id": null, 
            "errors": null, 
            "uuid": "0d87966a-b55d-4640-b836-974f9d10c803", 
            "tool_version": null, 
            "outputs": [], 
            "workflow_outputs": [
                {
                    "output_name": "output", 
                    "uuid": "fd9eb437-3aab-45c5-aed8-c65a0449c090", 
                    "label": null
                }
            ], 
            "annotation": "", 
            "content_id": null, 
            "input_connections": {}, 
            "inputs": [], 
            "position": {
                "top": 282.5, 
                "left": 200
            }, 
            "tool_state": "{\"collection_type\": \"list\"}", 
            "label": "Fastq read files", 
            "type": "data_collection_input", 
            "id": 0, 
            "name": "Input dataset collection"
        }, 
        "3": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", 
            "errors": null, 
            "uuid": "d89e8d50-3199-4276-9a1d-d654c73aad6a", 
            "tool_version": "1.4.1", 
            "outputs": [
                {
                    "type": "input", 
                    "name": "paired_output"
                }, 
                {
                    "type": "input", 
                    "name": "list_output"
                }, 
                {
                    "type": "input", 
                    "name": "out_file1"
                }, 
                {
                    "type": "_sniff_", 
                    "name": "paired_out_file"
                }
            ], 
            "post_job_actions": {
                "HideDatasetActionpaired_out_file": {
                    "output_name": "paired_out_file", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionlist_output": {
                    "output_name": "list_output", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionout_file1": {
                    "output_name": "out_file1", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionpaired_output": {
                    "output_name": "paired_output", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }
            }, 
            "workflow_outputs": [], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.1", 
            "input_connections": {
                "global_condition|inputs": {
                    "output_name": "output_unaligned_reads_l", 
                    "id": 2
                }
            }, 
            "inputs": [
                {
                    "name": "global_condition", 
                    "description": "runtime parameter for tool Concatenate multiple datasets"
                }
            ], 
            "position": {
                "top": 489.5, 
                "left": 1104
            }, 
            "tool_state": "{\"dataset_names\": \"\\\"false\\\"\", \"headers\": \"\\\"0\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"global_condition\": \"{\\\"__current_case__\\\": 0, \\\"input_type\\\": \\\"singles\\\", \\\"inputs\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", 
            "label": null, 
            "type": "tool", 
            "id": 3, 
            "tool_shed_repository": {
                "owner": "artbio", 
                "changeset_revision": "55cf9d9defd1", 
                "name": "concatenate_multiple_datasets", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Concatenate multiple datasets"
        }, 
        "2": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3", 
            "errors": null, 
            "uuid": "39957bf7-f0bc-4e5d-80fa-39f00b156f8d", 
            "tool_version": "2.3.4.3", 
            "outputs": [
                {
                    "type": "fastqsanger", 
                    "name": "output_unaligned_reads_l"
                }, 
                {
                    "type": "fastqsanger", 
                    "name": "output_aligned_reads_l"
                }, 
                {
                    "type": "fastqsanger", 
                    "name": "output_aligned_reads_r"
                }, 
                {
                    "type": "fastqsanger", 
                    "name": "output_unaligned_reads_r"
                }, 
                {
                    "type": "bam", 
                    "name": "output"
                }, 
                {
                    "type": "txt", 
                    "name": "mapping_stats"
                }
            ], 
            "post_job_actions": {
                "DeleteIntermediatesActionoutput_unaligned_reads_l": {
                    "output_name": "output_unaligned_reads_l", 
                    "action_type": "DeleteIntermediatesAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionoutput_unaligned_reads_r": {
                    "output_name": "output_unaligned_reads_r", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionoutput": {
                    "output_name": "output", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionoutput_aligned_reads_l": {
                    "output_name": "output_aligned_reads_l", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionmapping_stats": {
                    "output_name": "mapping_stats", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionoutput_aligned_reads_r": {
                    "output_name": "output_aligned_reads_r", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionoutput_unaligned_reads_l": {
                    "output_name": "output_unaligned_reads_l", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }
            }, 
            "workflow_outputs": [], 
            "annotation": "Get non-host reads", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3", 
            "input_connections": {
                "library|input_1": {
                    "output_name": "output", 
                    "id": 0
                }
            }, 
            "inputs": [
                {
                    "name": "library", 
                    "description": "runtime parameter for tool Bowtie2"
                }
            ], 
            "position": {
                "top": 337.5, 
                "left": 492
            }, 
            "tool_state": "{\"sam_options\": \"{\\\"__current_case__\\\": 1, \\\"sam_options_selector\\\": \\\"no\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"__current_case__\\\": 0, \\\"aligned_file\\\": \\\"false\\\", \\\"input_1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type\\\": \\\"single\\\", \\\"unaligned_file\\\": \\\"true\\\"}\", \"reference_genome\": \"{\\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\", \\\"source\\\": \\\"indexed\\\"}\", \"rg\": \"{\\\"__current_case__\\\": 3, \\\"rg_selector\\\": \\\"do_not_set\\\"}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"__current_case__\\\": 1, \\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"effort_options\\\": {\\\"__current_case__\\\": 1, \\\"effort_options_selector\\\": \\\"no\\\"}, \\\"input_options\\\": {\\\"__current_case__\\\": 0, \\\"input_options_selector\\\": \\\"yes\\\", \\\"int_quals\\\": \\\"false\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"skip\\\": \\\"0\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"trim3\\\": \\\"20\\\", \\\"trim5\\\": \\\"0\\\"}, \\\"other_options\\\": {\\\"__current_case__\\\": 1, \\\"other_options_selector\\\": \\\"no\\\"}, \\\"reporting_options\\\": {\\\"__current_case__\\\": 1, \\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\"}, \\\"scoring_options\\\": {\\\"__current_case__\\\": 1, \\\"scoring_options_selector\\\": \\\"no\\\"}}\"}", 
            "label": "Align to host", 
            "type": "tool", 
            "id": 2, 
            "tool_shed_repository": {
                "owner": "devteam", 
                "changeset_revision": "017aba02828d", 
                "name": "bowtie2", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Bowtie2"
        }, 
        "5": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4", 
            "errors": null, 
            "uuid": "1e362bf2-2d86-4ffb-9942-e9e3c23f48a7", 
            "tool_version": "2.8.4", 
            "outputs": [
                {
                    "type": "fasta", 
                    "name": "assembled_transcripts"
                }, 
                {
                    "type": "tabular", 
                    "name": "gene_to_trans"
                }
            ], 
            "post_job_actions": {
                "HideDatasetActionassembled_transcripts": {
                    "output_name": "assembled_transcripts", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActiongene_to_trans": {
                    "output_name": "gene_to_trans", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "RenameDatasetActionassembled_transcripts": {
                    "output_name": "assembled_transcripts", 
                    "action_type": "RenameDatasetAction", 
                    "action_arguments": {
                        "newname": "Assembled contigs"
                    }
                }
            }, 
            "workflow_outputs": [], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4", 
            "input_connections": {
                "pool|inputs|input": {
                    "output_name": "output", 
                    "id": 4
                }
            }, 
            "inputs": [
                {
                    "name": "additional_params", 
                    "description": "runtime parameter for tool Trinity"
                }
            ], 
            "position": {
                "top": 536.5, 
                "left": 2014
            }, 
            "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"norm\": \"\\\"false\\\"\", \"additional_params\": \"{\\\"guided\\\": {\\\"__current_case__\\\": 0, \\\"is_guided\\\": \\\"no\\\"}, \\\"long_reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"min_contig_length\\\": \\\"200\\\", \\\"min_kmer_cov\\\": \\\"1\\\"}\", \"pool\": \"{\\\"__current_case__\\\": 0, \\\"inputs\\\": {\\\"__current_case__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"paired_or_single\\\": \\\"single\\\", \\\"strand\\\": {\\\"__current_case__\\\": 0, \\\"is_strand_specific\\\": \\\"false\\\"}}, \\\"pool_mode\\\": \\\"Yes\\\"}\"}", 
            "label": "Assemble contigs using trinity", 
            "type": "tool", 
            "id": 5, 
            "tool_shed_repository": {
                "owner": "iuc", 
                "changeset_revision": "c9cfec002f71", 
                "name": "trinity", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Trinity"
        }, 
        "4": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/sequence_format_converter/sequence_format_converter/2.1.1", 
            "errors": null, 
            "uuid": "aacca937-880e-4827-bf4c-4aa64ff166f2", 
            "tool_version": "2.1.1", 
            "outputs": [
                {
                    "type": "fasta", 
                    "name": "output"
                }
            ], 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "output_name": "output", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }
            }, 
            "workflow_outputs": [], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/sequence_format_converter/sequence_format_converter/2.1.1", 
            "input_connections": {
                "input": {
                    "output_name": "out_file1", 
                    "id": 3
                }
            }, 
            "inputs": [
                {
                    "name": "input", 
                    "description": "runtime parameter for tool sequence_format_converter"
                }
            ], 
            "position": {
                "top": 524, 
                "left": 1621.5
            }, 
            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"output_format\": \"\\\"fastaw\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
            "label": "Collapse reads", 
            "type": "tool", 
            "id": 4, 
            "tool_shed_repository": {
                "owner": "artbio", 
                "changeset_revision": "f1d59113125a", 
                "name": "sequence_format_converter", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "sequence_format_converter"
        }, 
        "7": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", 
            "errors": null, 
            "uuid": "e08901b6-223f-4452-a02d-78bc87a25304", 
            "tool_version": "1.1", 
            "outputs": [
                {
                    "type": "fasta", 
                    "name": "output"
                }
            ], 
            "post_job_actions": {}, 
            "workflow_outputs": [
                {
                    "output_name": "output", 
                    "uuid": "f028d8bf-a8e1-413f-a476-474257bf90ee", 
                    "label": null
                }
            ], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", 
            "input_connections": {
                "input": {
                    "output_name": "out_file1", 
                    "id": 6
                }
            }, 
            "inputs": [
                {
                    "name": "input", 
                    "description": "runtime parameter for tool Filter sequences by length"
                }
            ], 
            "position": {
                "top": 408.5, 
                "left": 2600
            }, 
            "tool_state": "{\"__page__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", 
            "label": "Get contigs >5kb", 
            "type": "tool", 
            "id": 7, 
            "tool_shed_repository": {
                "owner": "devteam", 
                "changeset_revision": "2fd6033d0e9c", 
                "name": "fasta_filter_by_length", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Filter sequences by length"
        }, 
        "6": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", 
            "errors": null, 
            "uuid": "bdacf00f-3b5a-43b4-9dbf-2da4e87f8277", 
            "tool_version": "1.0.0", 
            "outputs": [
                {
                    "type": "input", 
                    "name": "out_file1"
                }
            ], 
            "post_job_actions": {
                "HideDatasetActionout_file1": {
                    "output_name": "out_file1", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }
            }, 
            "workflow_outputs": [], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.0", 
            "input_connections": {
                "input": {
                    "output_name": "assembled_transcripts", 
                    "id": 5
                }
            }, 
            "inputs": [
                {
                    "name": "input", 
                    "description": "runtime parameter for tool Regex Find And Replace"
                }
            ], 
            "position": {
                "top": 448.5, 
                "left": 2325
            }, 
            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"pattern\\\": \\\">(.+) len=(\\\\\\\\d+) .+\\\", \\\"replacement\\\": \\\">\\\\\\\\1_len=\\\\\\\\2\\\"}]\", \"__page__\": null}", 
            "label": "Change header format", 
            "type": "tool", 
            "id": 6, 
            "tool_shed_repository": {
                "owner": "galaxyp", 
                "changeset_revision": "209b7c5ee9d7", 
                "name": "regex_find_replace", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Regex Find And Replace"
        }, 
        "9": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/artbio/blastparser_and_hits/BlastParser_and_hits/2.6.1", 
            "errors": null, 
            "uuid": "e1e734ea-a9a9-41e0-aab4-685ccf3458b8", 
            "tool_version": "2.6.1", 
            "outputs": [
                {
                    "type": "tabular", 
                    "name": "tabularOutput"
                }, 
                {
                    "type": "fasta", 
                    "name": "fastaOutput"
                }, 
                {
                    "type": "fasta", 
                    "name": "al_sequences"
                }, 
                {
                    "type": "fasta", 
                    "name": "un_sequences"
                }
            ], 
            "post_job_actions": {
                "HideDatasetActional_sequences": {
                    "output_name": "al_sequences", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "RenameDatasetActiontabularOutput": {
                    "output_name": "tabularOutput", 
                    "action_type": "RenameDatasetAction", 
                    "action_arguments": {
                        "newname": "Contigs matching vir2"
                    }
                }, 
                "HideDatasetActionun_sequences": {
                    "output_name": "un_sequences", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }, 
                "HideDatasetActionfastaOutput": {
                    "output_name": "fastaOutput", 
                    "action_type": "HideDatasetAction", 
                    "action_arguments": {}
                }
            }, 
            "workflow_outputs": [
                {
                    "output_name": "tabularOutput", 
                    "uuid": "7e041eb9-86ad-4068-8f90-45e6b3e1a07e", 
                    "label": null
                }
            ], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/artbio/blastparser_and_hits/BlastParser_and_hits/2.6.1", 
            "input_connections": {
                "blast": {
                    "output_name": "output1", 
                    "id": 8
                }, 
                "sequences": {
                    "output_name": "output", 
                    "id": 7
                }
            }, 
            "inputs": [
                {
                    "name": "blast", 
                    "description": "runtime parameter for tool Parse blast output and compile hits"
                }, 
                {
                    "name": "sequences", 
                    "description": "runtime parameter for tool Parse blast output and compile hits"
                }
            ], 
            "position": {
                "top": 331, 
                "left": 3236
            }, 
            "tool_state": "{\"__page__\": null, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
            "label": null, 
            "type": "tool", 
            "id": 9, 
            "tool_shed_repository": {
                "owner": "artbio", 
                "changeset_revision": "b4c9c085d709", 
                "name": "blastparser_and_hits", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "Parse blast output and compile hits"
        }, 
        "8": {
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1", 
            "errors": null, 
            "uuid": "28cebda9-cd67-4c80-8a87-3a2a415326d9", 
            "tool_version": "0.3.1", 
            "outputs": [
                {
                    "type": "tabular", 
                    "name": "output1"
                }
            ], 
            "post_job_actions": {}, 
            "workflow_outputs": [
                {
                    "output_name": "output1", 
                    "uuid": "2a6f63d6-4915-4475-a5a1-a39b5b7b6993", 
                    "label": null
                }
            ], 
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1", 
            "input_connections": {
                "query": {
                    "output_name": "output", 
                    "id": 7
                }, 
                "db_opts|histdb": {
                    "output_name": "output", 
                    "id": 1
                }
            }, 
            "inputs": [
                {
                    "name": "db_opts", 
                    "description": "runtime parameter for tool NCBI BLAST+ blastx"
                }, 
                {
                    "name": "query", 
                    "description": "runtime parameter for tool NCBI BLAST+ blastx"
                }
            ], 
            "position": {
                "top": 508.5, 
                "left": 2908.5
            }, 
            "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\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
            "label": "Blastx vs vir2", 
            "type": "tool", 
            "id": 8, 
            "tool_shed_repository": {
                "owner": "devteam", 
                "changeset_revision": "e25d3acf6e68", 
                "name": "ncbi_blast_plus", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "name": "NCBI BLAST+ blastx"
        }
    }, 
    "annotation": "", 
    "name": "Metavisitor: Trinity test in Use Case 2-2"
}