[
    {
        "name": "Vsearch",
        "docker_name": "vsearch",
        "description": "Get OTU from metabarcoding reads with Vsearch",
        "version": "0.0.1",
        "author": "MBB",
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "steps_in": [
            {
                "step_name": "VSEARCH_5",
                "tool_name": "VSEARCH_mergepairs",
                "rule_name": "VSEARCH_mergepairs",
                "params": [
                    {
                        "input_name": "read_dir",
                        "origin_command": "raw_read_dir",
                        "origin_name": "read_dir",
                        "origin_step": "input"
                    }
                ]
            },
            {
                "step_name": "VSEARCH_2",
                "tool_name": "VSEARCH_filter",
                "rule_name": "VSEARCH_filter",
                "params": [
                    {
                        "input_name": "read_dir",
                        "origin_command": "VSEARCH_mergepairs",
                        "origin_name": "mergepairs_done",
                        "origin_step": "VSEARCH_5"
                    }
                ]
            },
            {
                "step_name": "VSEARCH",
                "tool_name": "VSEARCH_derep",
                "rule_name": "VSEARCH_derep",
                "params": [
                    {
                        "input_name": "fasta_dir",
                        "origin_command": "VSEARCH_filter",
                        "origin_name": "filter_done",
                        "origin_step": "VSEARCH_2"
                    }
                ]
            },
            {
                "step_name": "format_conversion",
                "tool_name": "fastamerge",
                "rule_name": "fastamerge",
                "params": [
                    {
                        "input_name": "fasta_dir",
                        "origin_command": "VSEARCH_derep",
                        "origin_name": "derepfasta_dir",
                        "origin_step": "VSEARCH"
                    }
                ]
            },
            {
                "step_name": "VSEARCH_3",
                "tool_name": "VSEARCH_derep_fastafile",
                "rule_name": "VSEARCH_derep_fastafile",
                "params": [
                    {
                        "input_name": "fasta",
                        "origin_command": "fastamerge",
                        "origin_name": "fasta",
                        "origin_step": "format_conversion"
                    }
                ]
            },
            {
                "step_name": "VSEARCH_4",
                "tool_name": "VSEARCH_clust_unoise_OTU",
                "rule_name": "VSEARCH_clust_unoise_OTU",
                "params": [
                    {
                        "input_name": "fasta",
                        "origin_command": "VSEARCH_derep_fastafile",
                        "origin_name": "derepfasta",
                        "origin_step": "VSEARCH_3"
                    },
                    {
                        "input_name": "ucfile",
                        "origin_command": "VSEARCH_derep_fastafile",
                        "origin_name": "uclust_like",
                        "origin_step": "VSEARCH_3"
                    },
                    {
                        "input_name": "allfasta",
                        "origin_command": "fastamerge",
                        "origin_name": "fasta",
                        "origin_step": "format_conversion"
                    }
                ]
            },
            {
                "step_name": "metabarcoding",
                "tool_name": "dada2_assign_taxonomy",
                "rule_name": "dada2_assign_taxonomy",
                "params": [
                    {
                        "input_name": "seqs",
                        "origin_command": "VSEARCH_clust_unoise_OTU",
                        "origin_name": "centroids",
                        "origin_step": "VSEARCH_4"
                    },
                    {
                        "input_name": "abundance",
                        "origin_command": "VSEARCH_clust_unoise_OTU",
                        "origin_name": "otutab",
                        "origin_step": "VSEARCH_4"
                    }
                ]
            }
        ],
        "steps": [
            {
                "title": "VSEARCH_5",
                "name": "VSEARCH_5",
                "tools": [
                    "VSEARCH_mergepairs"
                ],
                "default": "VSEARCH_mergepairs"
            },
            {
                "title": "VSEARCH_2",
                "name": "VSEARCH_2",
                "tools": [
                    "VSEARCH_filter"
                ],
                "default": "VSEARCH_filter"
            },
            {
                "title": "VSEARCH",
                "name": "VSEARCH",
                "tools": [
                    "VSEARCH_derep"
                ],
                "default": "VSEARCH_derep"
            },
            {
                "title": "format_conversion",
                "name": "format_conversion",
                "tools": [
                    "fastamerge"
                ],
                "default": "fastamerge"
            },
            {
                "title": "VSEARCH_3",
                "name": "VSEARCH_3",
                "tools": [
                    "VSEARCH_derep_fastafile"
                ],
                "default": "VSEARCH_derep_fastafile"
            },
            {
                "title": "VSEARCH_4",
                "name": "VSEARCH_4",
                "tools": [
                    "VSEARCH_clust_unoise_OTU"
                ],
                "default": "VSEARCH_clust_unoise_OTU"
            },
            {
                "title": "metabarcoding",
                "name": "metabarcoding",
                "tools": [
                    "dada2_assign_taxonomy"
                ],
                "default": "dada2_assign_taxonomy"
            }
        ],
        "input": [
            "raw_read_dir"
        ],
        "params_equals": [],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/vsearch",
        "json": {
            "class": "GraphLinksModel",
            "linkFromPortIdProperty": "fromPort",
            "linkToPortIdProperty": "toPort",
            "modelData": {
                "position": "-482.614990234375 -1017"
            },
            "nodeDataArray": [
                {
                    "name": "VSEARCH_derep",
                    "text": "VSEARCH Dereplicate",
                    "size2": "185 85",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta_dir",
                            "value": "fasta_dir",
                            "description": "Directory containing fasta files *.fasta *.fas *.fa",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "derepfasta_done",
                            "value": "derepfasta_done",
                            "description": "stats after fasta files dereplication",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "o2",
                            "type": "fasta_dir",
                            "value": "derepfasta_dir",
                            "description": "dir containing dereplicated fasta files",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o3",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Conversion of an aligned fasta file to phylip format",
                    "version": "2.21.1",
                    "key": "5008666689",
                    "loc": "310 -700"
                },
                {
                    "name": "VSEARCH_filter",
                    "text": "VSEARCH Filter",
                    "size2": "155 60",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "read_dir",
                            "value": "read_dir",
                            "description": "Directory containing read dir files *.fastq.gz *.fq.gz",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fasta_dir",
                            "value": "filter_done",
                            "description": "dir containing filtered fasta files",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Filter fastqc reads and produce fasta files",
                    "version": "2.21.1",
                    "key": "5939661377",
                    "loc": "60 -780"
                },
                {
                    "name": "read_dir",
                    "text": "read_dir",
                    "size2": "",
                    "category": "Data",
                    "strokeWidth": 2,
                    "fill": "#2ecc71",
                    "inservices": [],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "read_dir",
                            "value": "raw_read_dir",
                            "description": "",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "unknown",
                    "version": "unknown",
                    "key": -9,
                    "loc": "-380 -890"
                },
                {
                    "name": "fastamerge",
                    "text": "fasta merge",
                    "size2": "155 60",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta_dir",
                            "value": "fasta_dir",
                            "description": "",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fasta_file",
                            "value": "fasta",
                            "description": "merged fasta file",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Concatenate fasta files in a dir in a single fasta file",
                    "version": "unknown",
                    "key": "3952800598",
                    "loc": "460 -830"
                },
                {
                    "name": "VSEARCH_derep_fastafile",
                    "text": "VSEARCH Dereplicate file",
                    "size2": "220 85",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta_file",
                            "value": "fasta",
                            "description": "fasta file ",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fasta_file",
                            "value": "derepfasta",
                            "description": "dereplicated sequences in fasta format sorted by decreasing abundance.",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "o2",
                            "type": "tsv",
                            "value": "uclust_like",
                            "description": "tab-separated uclust-like format with 10 columns and 3 different type of entries (S, H or C)",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o3",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Merge strictly identical sequences contained in fasta file",
                    "version": "2.21.1",
                    "key": "5407894253",
                    "loc": "600 -1070"
                },
                {
                    "name": "VSEARCH_clust_unoise_OTU",
                    "text": "VSEARCH Unoise rm chimera OTU",
                    "size2": "310 110",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta_file",
                            "value": "fasta",
                            "description": "dereplicated fasta file",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "i2",
                            "type": "tsv",
                            "value": "ucfile",
                            "description": "uc file for dereplicated",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "i3",
                            "type": "fasta_file",
                            "value": "allfasta",
                            "description": "all fasta file before dereplication",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fasta_file",
                            "value": "centroids",
                            "description": "Fasta Clustered, denovo chimera removed and relabel with OTU_n",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "o2",
                            "type": "tsv",
                            "value": "otutab",
                            "description": "OTU table",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o3",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Denoising of the fasta sequences in filename according to the UNOISE3 algorithm (Robert Edgar), chimera removal and OTU output",
                    "version": "2.21.1",
                    "key": "5983630227",
                    "loc": "1030 -890"
                },
                {
                    "name": "VSEARCH_mergepairs",
                    "text": "VSEARCH MergePairs",
                    "size2": "185 60",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "read_dir",
                            "value": "read_dir",
                            "description": "Directory containing read dir files *.fastq.gz *.fq.gz",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "read_dir",
                            "value": "mergepairs_done",
                            "description": "dir containing merged fastq files",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Merge paired-end reads into one sequence",
                    "version": "2.21.1",
                    "key": "1833319893",
                    "loc": "-160 -890"
                },
                {
                    "name": "dada2_assign_taxonomy",
                    "text": "dada2_assign_taxonomy",
                    "size2": "200 85",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta_file",
                            "value": "seqs",
                            "description": "",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "i2",
                            "type": "tsv",
                            "value": "abundance",
                            "description": "per sample OTU abundance ",
                            "ptype": "IN",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "tsv",
                            "value": "taxa_bootstrap",
                            "description": "Bootstap support table",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        },
                        {
                            "name": "o2",
                            "type": "tsv",
                            "value": "taxa_assigment",
                            "description": "Matrix with each row corresponding to an input sequence, and each column corresponding to a taxonomic level",
                            "ptype": "OUT",
                            "from": "",
                            "list": false,
                            "stroke": "#000000"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o3",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Fast and accurate sample inference from amplicon data with single-nucleotide resolution",
                    "version": "1.16",
                    "key": "9893922709",
                    "loc": "1440 -600"
                }
            ],
            "linkDataArray": [
                {
                    "from": "5939661377",
                    "to": "5008666689",
                    "fromPort": "filter_done",
                    "toPort": "fasta_dir",
                    "points": [
                        150.64453125,
                        -776.1,
                        160.64453125,
                        -776.1,
                        177.5,
                        -776.1,
                        177.5,
                        -697.35,
                        194.35546875,
                        -697.35,
                        204.35546875,
                        -697.35
                    ]
                },
                {
                    "from": "5008666689",
                    "to": "3952800598",
                    "fromPort": "derepfasta_dir",
                    "toPort": "fasta_dir",
                    "points": [
                        415.64453125,
                        -685.811083984375,
                        425.64453125,
                        -685.811083984375,
                        425.64453125,
                        -771.25,
                        359.35546875,
                        -771.25,
                        359.35546875,
                        -826.1,
                        369.35546875,
                        -826.1
                    ]
                },
                {
                    "from": "3952800598",
                    "to": "5407894253",
                    "fromPort": "fasta",
                    "toPort": "fasta",
                    "points": [
                        550.64453125,
                        -828.9463053385417,
                        560.64453125,
                        -828.9463053385417,
                        560.64453125,
                        -943.75,
                        466.85546875,
                        -943.75,
                        466.85546875,
                        -1067.35,
                        476.85546875,
                        -1067.35
                    ]
                },
                {
                    "from": "3952800598",
                    "to": "5983630227",
                    "fromPort": "fasta",
                    "toPort": "allfasta",
                    "points": [
                        550.64453125,
                        -823.2536946614583,
                        568.64453125,
                        -823.2536946614583,
                        710.25,
                        -823.2536946614583,
                        710.25,
                        -865.52216796875,
                        851.85546875,
                        -865.52216796875,
                        861.85546875,
                        -865.52216796875
                    ]
                },
                {
                    "from": "5407894253",
                    "to": "5983630227",
                    "fromPort": "derepfasta",
                    "toPort": "fasta",
                    "points": [
                        723.14453125,
                        -1078.888916015625,
                        733.14453125,
                        -1078.888916015625,
                        792.5,
                        -1078.888916015625,
                        792.5,
                        -911.67783203125,
                        851.85546875,
                        -911.67783203125,
                        861.85546875,
                        -911.67783203125
                    ]
                },
                {
                    "from": "5407894253",
                    "to": "5983630227",
                    "fromPort": "uclust_like",
                    "toPort": "ucfile",
                    "points": [
                        723.14453125,
                        -1055.8110839843753,
                        733.14453125,
                        -1055.8110839843753,
                        792.5,
                        -1055.8110839843753,
                        792.5,
                        -888.6,
                        851.85546875,
                        -888.6,
                        861.85546875,
                        -888.6
                    ]
                },
                {
                    "from": -9,
                    "to": "1833319893",
                    "fromPort": "raw_read_dir",
                    "toPort": "read_dir",
                    "points": [
                        -322.385009765625,
                        -888.7,
                        -312.385009765625,
                        -888.7,
                        -294.0147705078125,
                        -888.7,
                        -294.0147705078125,
                        -886.1,
                        -275.64453125,
                        -886.1,
                        -265.64453125,
                        -886.1
                    ]
                },
                {
                    "from": "1833319893",
                    "to": "5939661377",
                    "fromPort": "mergepairs_done",
                    "toPort": "read_dir",
                    "points": [
                        -54.35546875,
                        -886.1,
                        -44.35546875,
                        -886.1,
                        -42.5,
                        -886.1,
                        -42.5,
                        -776.1,
                        -40.64453125,
                        -776.1,
                        -30.64453125,
                        -776.1
                    ]
                },
                {
                    "from": "5983630227",
                    "to": "9893922709",
                    "fromPort": "centroids",
                    "toPort": "seqs",
                    "points": [
                        1198.14453125,
                        -900.138916015625,
                        1208.14453125,
                        -900.138916015625,
                        1262.5,
                        -900.138916015625,
                        1262.5,
                        -608.888916015625,
                        1316.85546875,
                        -608.888916015625,
                        1326.85546875,
                        -608.888916015625
                    ]
                },
                {
                    "from": "5983630227",
                    "to": "9893922709",
                    "fromPort": "otutab",
                    "toPort": "abundance",
                    "points": [
                        1198.14453125,
                        -877.061083984375,
                        1208.14453125,
                        -877.061083984375,
                        1262.5,
                        -877.061083984375,
                        1262.5,
                        -585.811083984375,
                        1316.85546875,
                        -585.811083984375,
                        1326.85546875,
                        -585.811083984375
                    ]
                }
            ],
            "version": 2
        },
        "yaml": "{\nname: \"Vsearch\",\ndocker_name: \"vsearch\",\ndescription: \"Get OTU from metabarcoding reads with Vsearch\",\nversion: \"0.0.1\",\nauthor: \"MBB\",\noptions: [\n    {\n    name: \"results_dir\",\n    type: \"output_dir\",\n    value: \"\/Results\",\n    label: \"Results directory: \",\n    volumes:  [Results: \"\/Results\"]\n    },\n],\nsteps_in: [\n{ step_name: \"VSEARCH_5\", tool_name: \"VSEARCH_mergepairs\", rule_name: \"VSEARCH_mergepairs\",\n    params: [\n        { input_name: read_dir, origin_command: raw_read_dir, origin_name: read_dir, origin_step: input},\n    ]\n},\n{ step_name: \"VSEARCH_2\", tool_name: \"VSEARCH_filter\", rule_name: \"VSEARCH_filter\",\n    params: [\n        { input_name: read_dir, origin_command: VSEARCH_mergepairs, origin_name: mergepairs_done, origin_step: VSEARCH_5},\n    ]\n},\n{ step_name: \"VSEARCH\", tool_name: \"VSEARCH_derep\", rule_name: \"VSEARCH_derep\",\n    params: [\n        { input_name: fasta_dir, origin_command: VSEARCH_filter, origin_name: filter_done, origin_step: VSEARCH_2},\n    ]\n},\n{ step_name: \"format_conversion\", tool_name: \"fastamerge\", rule_name: \"fastamerge\",\n    params: [\n        { input_name: fasta_dir, origin_command: VSEARCH_derep, origin_name: derepfasta_dir, origin_step: VSEARCH},\n    ]\n},\n{ step_name: \"VSEARCH_3\", tool_name: \"VSEARCH_derep_fastafile\", rule_name: \"VSEARCH_derep_fastafile\",\n    params: [\n        { input_name: fasta, origin_command: fastamerge, origin_name: fasta, origin_step: format_conversion},\n    ]\n},\n{ step_name: \"VSEARCH_4\", tool_name: \"VSEARCH_clust_unoise_OTU\", rule_name: \"VSEARCH_clust_unoise_OTU\",\n    params: [\n        { input_name: fasta, origin_command: VSEARCH_derep_fastafile, origin_name: derepfasta, origin_step: VSEARCH_3},\n        { input_name: ucfile, origin_command: VSEARCH_derep_fastafile, origin_name: uclust_like, origin_step: VSEARCH_3},\n        { input_name: allfasta, origin_command: fastamerge, origin_name: fasta, origin_step: format_conversion},\n    ]\n},\n{ step_name: \"metabarcoding\", tool_name: \"dada2_assign_taxonomy\", rule_name: \"dada2_assign_taxonomy\",\n    params: [\n        { input_name: seqs, origin_command: VSEARCH_clust_unoise_OTU, origin_name: centroids, origin_step: VSEARCH_4},\n        { input_name: abundance, origin_command: VSEARCH_clust_unoise_OTU, origin_name: otutab, origin_step: VSEARCH_4},\n    ]\n},\n],\nsteps: [\n    { title: \"VSEARCH_5\", name: \"VSEARCH_5\", tools: [VSEARCH_mergepairs], default: \"VSEARCH_mergepairs\" },\n    { title: \"VSEARCH_2\", name: \"VSEARCH_2\", tools: [VSEARCH_filter], default: \"VSEARCH_filter\" },\n    { title: \"VSEARCH\", name: \"VSEARCH\", tools: [VSEARCH_derep], default: \"VSEARCH_derep\" },\n    { title: \"format_conversion\", name: \"format_conversion\", tools: [fastamerge], default: \"fastamerge\" },\n    { title: \"VSEARCH_3\", name: \"VSEARCH_3\", tools: [VSEARCH_derep_fastafile], default: \"VSEARCH_derep_fastafile\" },\n    { title: \"VSEARCH_4\", name: \"VSEARCH_4\", tools: [VSEARCH_clust_unoise_OTU], default: \"VSEARCH_clust_unoise_OTU\" },\n    { title: \"metabarcoding\", name: \"metabarcoding\", tools: [dada2_assign_taxonomy], default: \"dada2_assign_taxonomy\" },\n],\ninput: [\"raw_read_dir\",],\nparams_equals: [\n\n]\n}\n"
    }
]