annotate Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga @ 0:4a47903bb4df draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit f6fa4bd2f176e3f4ae4b9c887113557d3c4ff209

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Metavisitor: Workflow for Use Case 3-2", 
    "steps": {
        "0": {
            "annotation": "", 
            "content_id": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Patient sequences collection"
                }
            ], 
            "label": null, 
            "name": "Input dataset collection", 
            "outputs": [], 
            "position": {
                "left": 116.09375, 
                "top": 130.59375
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"collection_type\": \"list\", \"name\": \"Patient sequences collection\"}", 
            "tool_version": null, 
            "type": "data_collection_input", 
            "uuid": "4c996dac-b8a2-4b4c-bb98-ab708c076e4e", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "13712bd9-2bed-4542-8137-737866b8537a"
                }
            ]
        }, 
        "1": {
            "annotation": "", 
            "content_id": null, 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Nucleotide Viral BLAST database"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 1352.578125, 
                "top": 992.578125
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Nucleotide Viral BLAST database\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "39d691fe-ba93-4eb1-a714-4133f03728b1", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "d92490ff-273f-4145-bc3d-ade5fca45255"
                }
            ]
        }, 
        "2": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", 
            "id": 2, 
            "input_connections": {
                "library|input_1": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Bowtie2", 
            "outputs": [
                {
                    "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": "fastqsanger"
                }, 
                {
                    "name": "output", 
                    "type": "bam"
                }, 
                {
                    "name": "output_sam", 
                    "type": "sam"
                }, 
                {
                    "name": "mapping_stats", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 426.5625, 
                "top": 258.609375
            }, 
            "post_job_actions": {
                "DeleteIntermediatesActionoutput_unaligned_reads_l": {
                    "action_arguments": {}, 
                    "action_type": "DeleteIntermediatesAction", 
                    "output_name": "output_unaligned_reads_l"
                }, 
                "HideDatasetActionmapping_stats": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "mapping_stats"
                }, 
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }, 
                "HideDatasetActionoutput_aligned_reads_r": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_aligned_reads_r"
                }, 
                "HideDatasetActionoutput_sam": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_sam"
                }, 
                "HideDatasetActionoutput_unaligned_reads_l": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_unaligned_reads_l"
                }, 
                "HideDatasetActionoutput_unaligned_reads_r": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_unaligned_reads_r"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"True\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg19\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"True\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", 
            "tool_version": "2.2.6.2", 
            "type": "tool", 
            "uuid": "76fe9f4e-cf0b-4480-aadf-ba461c595414", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output_aligned_reads_l", 
                    "uuid": "ec776ac8-cd59-4d76-9ad8-d82905393ad7"
                }
            ]
        }, 
        "3": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", 
            "id": 3, 
            "input_connections": {
                "library|input_1": {
                    "id": 2, 
                    "output_name": "output_unaligned_reads_l"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Bowtie2", 
            "outputs": [
                {
                    "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": "fastqsanger"
                }, 
                {
                    "name": "output", 
                    "type": "bam"
                }, 
                {
                    "name": "output_sam", 
                    "type": "sam"
                }, 
                {
                    "name": "mapping_stats", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 776.53125, 
                "top": 379.59375
            }, 
            "post_job_actions": {
                "DeleteIntermediatesActionoutput_unaligned_reads_l": {
                    "action_arguments": {}, 
                    "action_type": "DeleteIntermediatesAction", 
                    "output_name": "output_unaligned_reads_l"
                }, 
                "HideDatasetActionmapping_stats": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "mapping_stats"
                }, 
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }, 
                "HideDatasetActionoutput_aligned_reads_r": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_aligned_reads_r"
                }, 
                "HideDatasetActionoutput_sam": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_sam"
                }, 
                "HideDatasetActionoutput_unaligned_reads_l": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_unaligned_reads_l"
                }, 
                "HideDatasetActionoutput_unaligned_reads_r": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_unaligned_reads_r"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"True\\\", \\\"unaligned_file\\\": \\\"False\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"vir1\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"True\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", 
            "tool_version": "2.2.6.2", 
            "type": "tool", 
            "uuid": "5f6b3d0e-06eb-4e75-9139-b41a4d88f79a", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output_aligned_reads_l", 
                    "uuid": "5ab6ffef-583a-4509-9732-41075eb5ed98"
                }
            ]
        }, 
        "4": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 3, 
                    "output_name": "output_aligned_reads_l"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "FASTQ to FASTA", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1132.09375, 
                "top": 572.609375
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", 
            "tool_state": "{\"input\": \"null\", \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"-n\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "uuid": "7a97429a-2900-49f1-b218-35c650a71390", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "72347b83-e33d-48e0-950e-4f9ea61d14ea"
                }
            ]
        }, 
        "5": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
            "id": 5, 
            "input_connections": {
                "inputs_0|input": {
                    "id": 4, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Oases_optimiser", 
            "outputs": [
                {
                    "name": "transcripts", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1346.5625, 
                "top": 731.578125
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
            "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"69\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", 
            "tool_version": "1.1.4", 
            "type": "tool", 
            "uuid": "b525a58a-dd2d-48c4-ac0e-516184a53ced", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "transcripts", 
                    "uuid": "f51ee1b3-fcfe-4db4-b341-713c1f7590dd"
                }
            ]
        }, 
        "6": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", 
            "id": 6, 
            "input_connections": {
                "db_opts|histdb": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "query": {
                    "id": 5, 
                    "output_name": "transcripts"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "NCBI BLAST+ blastn", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 1579.5625, 
                "top": 887.59375
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", 
            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastn\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"query\": \"null\"}", 
            "tool_version": "0.1.07", 
            "type": "tool", 
            "uuid": "da354a9b-03b3-4aa9-b409-0689f6a3e15b", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output1", 
                    "uuid": "a63b93b5-5870-4e7b-81bc-345ede8af734"
                }
            ]
        }, 
        "7": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 
            "id": 7, 
            "input_connections": {
                "blast": {
                    "id": 6, 
                    "output_name": "output1"
                }, 
                "sequences": {
                    "id": 5, 
                    "output_name": "transcripts"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Parse blast output and compile hits", 
            "outputs": [
                {
                    "name": "tabularOutput", 
                    "type": "tabular"
                }, 
                {
                    "name": "fastaOutput", 
                    "type": "fasta"
                }, 
                {
                    "name": "al_sequences", 
                    "type": "fasta"
                }, 
                {
                    "name": "un_sequences", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1893.5625, 
                "top": 649.59375
            }, 
            "post_job_actions": {
                "HideDatasetActional_sequences": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "al_sequences"
                }, 
                "HideDatasetActionfastaOutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "fastaOutput"
                }, 
                "HideDatasetActionun_sequences": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "un_sequences"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 
            "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"Patent\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", 
            "tool_version": "2.4.3", 
            "type": "tool", 
            "uuid": "a2b3cb8f-ce9e-4a65-913c-44adbb1f2b41", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "tabularOutput", 
                    "uuid": "beee945b-3fb7-4340-a727-06c3146717bf"
                }
            ]
        }, 
        "8": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "tabularOutput"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Concatenate multiple datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 2231.5, 
                "top": 744.5
            }, 
            "post_job_actions": {
                "RenameDatasetActionout_file1": {
                    "action_arguments": {
                        "newname": "Virus identification by patient"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "0.2", 
            "type": "tool", 
            "uuid": "9a01734f-c0e7-42c2-b7d6-6ed69bcf728e", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "out_file1", 
                    "uuid": "a177238a-37d7-469b-a243-1330acc04024"
                }
            ]
        }
    }, 
    "uuid": "c56c85ae-7cca-44ff-b732-50f75db00d0b"
}