view Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga @ 2:48b020a0d2f7 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Metavisitor: Workflow for Use Case 2-2", 
    "steps": {
        "0": {
            "annotation": "", 
            "content_id": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Input Dataset Collection"
                }
            ], 
            "label": null, 
            "name": "Input dataset collection", 
            "outputs": [], 
            "position": {
                "left": 199.91314697265625, 
                "top": 183.5937557220459
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", 
            "tool_version": null, 
            "type": "data_collection_input", 
            "uuid": "3b7db228-7d72-4b8a-9296-5e51ceda8cdd", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "dd803215-4fa9-4444-83df-06e42912b545"
                }
            ]
        }, 
        "1": {
            "annotation": "", 
            "content_id": null, 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Protein Blast database"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 1887.9861450195312, 
                "top": 619.5659847259521
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Protein Blast database\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "9f28fc2b-f552-4021-b6fc-ba95f6f3e8dd", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "8d19a7b0-6b52-46ee-be47-cce18eca9453"
                }
            ]
        }, 
        "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": 433.48956298828125, 
                "top": 367.6389217376709
            }, 
            "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_l": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_aligned_reads_l"
                }, 
                "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_shed_repository": {
                "changeset_revision": "a9d4f71dbfb0", 
                "name": "bowtie2", 
                "owner": "devteam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "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\\\": \\\"AgamP4\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"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\\\": {\\\"int_quals\\\": \\\"false\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}", 
            "tool_version": "2.2.6.2", 
            "type": "tool", 
            "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126", 
            "workflow_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", 
            "id": 3, 
            "input_connections": {
                "input": {
                    "id": 2, 
                    "output_name": "output_unaligned_reads_l"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "FASTQ to FASTA", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 774.4097290039062, 
                "top": 315.97223472595215
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", 
            "tool_shed_repository": {
                "changeset_revision": "186b8d913e6c", 
                "name": "fastq_to_fasta", 
                "owner": "devteam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "uuid": "71496d9a-5490-46a7-930d-37ec45d1ccb8", 
            "workflow_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
            "id": 4, 
            "input_connections": {
                "input": {
                    "id": 3, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Concatenate multiple datasets", 
            "outputs": [
                {
                    "name": "out_file1", 
                    "type": "input"
                }
            ], 
            "position": {
                "left": 1005.4166717529297, 
                "top": 303.00348472595215
            }, 
            "post_job_actions": {
                "ChangeDatatypeActionout_file1": {
                    "action_arguments": {
                        "newtype": "fasta"
                    }, 
                    "action_type": "ChangeDatatypeAction", 
                    "output_name": "out_file1"
                }, 
                "HideDatasetActionout_file1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
            "tool_shed_repository": {
                "changeset_revision": "201c568972c3", 
                "name": "concatenate_multiple_datasets", 
                "owner": "mvdbeek", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
            "tool_version": "0.2", 
            "type": "tool", 
            "uuid": "26ef2a8f-e79e-4e04-92d7-7629b56a3765", 
            "workflow_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
            "id": 5, 
            "input_connections": {
                "switch|input": {
                    "id": 4, 
                    "output_name": "out_file1"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "fasta - tabular", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1290.5555725097656, 
                "top": 296.59723472595215
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
            "tool_shed_repository": {
                "changeset_revision": "330dd8a8c31a", 
                "name": "msp_fasta_tabular_converter", 
                "owner": "drosofff", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "uuid": "1d78a822-0e08-4e92-a9f7-bc80166e36a1", 
            "workflow_outputs": []
        }, 
        "6": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
            "id": 6, 
            "input_connections": {
                "switch|input": {
                    "id": 5, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "fasta - tabular", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1517.5521240234375, 
                "top": 302.5868282318115
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
            "tool_shed_repository": {
                "changeset_revision": "330dd8a8c31a", 
                "name": "msp_fasta_tabular_converter", 
                "owner": "drosofff", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "uuid": "d6d8e36c-641a-4662-b615-0745b9d9fb55", 
            "workflow_outputs": []
        }, 
        "7": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
            "id": 7, 
            "input_connections": {
                "inputs_0|input": {
                    "id": 6, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Oases_optimiser", 
            "outputs": [
                {
                    "name": "transcripts", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1778.4375610351562, 
                "top": 339.0625057220459
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
            "tool_shed_repository": {
                "changeset_revision": "f08d9c814ffb", 
                "name": "msp_oases", 
                "owner": "drosofff", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"end_hash_length\": \"\\\"69\\\"\", \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"start_hash_length\": \"\\\"25\\\"\"}", 
            "tool_version": "1.1.4", 
            "type": "tool", 
            "uuid": "98ece8ec-729a-41a1-a61e-f6fcfce0e835", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "transcripts", 
                    "uuid": "e679f97f-a15b-479d-9154-59cd57642674"
                }
            ]
        }, 
        "8": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", 
            "id": 8, 
            "input_connections": {
                "input": {
                    "id": 7, 
                    "output_name": "transcripts"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Filter sequences by length", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "fasta"
                }
            ], 
            "position": {
                "left": 1956.4236450195312, 
                "top": 213.05556297302246
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", 
            "tool_shed_repository": {
                "changeset_revision": "c8cd0a03db49", 
                "name": "fasta_filter_by_length", 
                "owner": "devteam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", 
            "tool_version": "1.1", 
            "type": "tool", 
            "uuid": "db1f7d30-3b47-4030-9724-e371e0ec54a1", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output", 
                    "uuid": "0b517cd3-6991-4968-91e3-894446dd6d8b"
                }
            ]
        }, 
        "9": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", 
            "id": 9, 
            "input_connections": {
                "db_opts|histdb": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "query": {
                    "id": 8, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "NCBI BLAST+ blastx", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "tabular"
                }
            ], 
            "position": {
                "left": 2225.451416015625, 
                "top": 313.00348472595215
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", 
            "tool_shed_repository": {
                "changeset_revision": "577d9c12411a", 
                "name": "ncbi_blast_plus", 
                "owner": "devteam", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"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\\\"]}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
            "tool_version": "0.1.06", 
            "type": "tool", 
            "uuid": "b151f8e8-c81b-466a-8a31-d4b42d4b95e9", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "output1", 
                    "uuid": "65223b13-b6fa-45ae-a927-bb96b184bb75"
                }
            ]
        }, 
        "10": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 
            "id": 10, 
            "input_connections": {
                "blast": {
                    "id": 9, 
                    "output_name": "output1"
                }, 
                "sequences": {
                    "id": 8, 
                    "output_name": "output"
                }
            }, 
            "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": 2559.5313720703125, 
                "top": 128.57639122009277
            }, 
            "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_shed_repository": {
                "changeset_revision": "6dfa79a6908a", 
                "name": "msp_blastparser_and_hits", 
                "owner": "drosofff", 
                "tool_shed": "toolshed.g2.bx.psu.edu"
            }, 
            "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", 
            "tool_version": "2.4.3", 
            "type": "tool", 
            "uuid": "30288e33-ff64-4089-9b45-428027744176", 
            "workflow_outputs": [
                {
                    "label": null, 
                    "output_name": "tabularOutput", 
                    "uuid": "6b25acfc-474c-4852-b196-a14a4cf619e3"
                }
            ]
        }
    }, 
    "uuid": "ea5b1974-4efa-4a30-a29c-4cfa9fd7da83"
}