[
    {
        "id": "FROGS_filter_OTU",
        "name": "FROGS filter OTU",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Filters OTUs on several criteria",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "generic_iframe",
        "commands": [
            {
                "name": "FROGS_filter_OTU",
                "command": "cluster_filters.py",
                "category": "FROGS",
                "output_dir": "FROGS_filter_OTU",
                "inputs": [
                    {
                        "name": "sequence_file",
                        "type": "fasta_file",
                        "description": "the sequences in fasta format"
                    },
                    {
                        "name": "biom",
                        "type": "biom",
                        "description": "The abundance of each OTU in each sample"
                    }
                ],
                "outputs": [
                    {
                        "name": "filtered_sequences",
                        "file": "otuFilter_sequences.fasta",
                        "type": "fasta_file",
                        "description": "The sequences after filtering"
                    },
                    {
                        "name": "abundance_file",
                        "file": "otuFilter_abundance.biom",
                        "type": "biom",
                        "description": "The abundance after filtering"
                    },
                    {
                        "name": "excluded_file",
                        "file": "excluded.tsv",
                        "type": "tsv",
                        "description": "The list of the OTUs deleted by filters"
                    },
                    {
                        "name": "summary",
                        "file": "filtOTU_report.html",
                        "type": "html",
                        "description": "The filters and the number of removed sequences"
                    }
                ],
                "options": [
                    {
                        "name": "FROGS_filter_OTU_threads",
                        "prefix": "-p",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "FROGS_filter_OTU_min_sample_presence",
                        "prefix": null,
                        "type": "numeric",
                        "value": 0,
                        "min": 2,
                        "max": "NA",
                        "step": "NA",
                        "label": "Fill the field only if you want this treatment. Keep OTU if it is present in at least this number of samples."
                    },
                    {
                        "name": "FROGS_filter_OTU_min_abundance_proportion",
                        "prefix": null,
                        "type": "numeric",
                        "value": 5.0e-5,
                        "min": 0,
                        "max": 1,
                        "step": "NA",
                        "label": "Minimum proportion of sequences abundancy to keep OTU."
                    },
                    {
                        "name": "FROGS_filter_OTU_nb_biggest_otu",
                        "prefix": null,
                        "type": "numeric",
                        "value": 300,
                        "min": 0,
                        "max": "NA",
                        "step": "NA",
                        "label": "Fill the fields only if you want this treatment. Keep the N biggest OTU"
                    },
                    {
                        "name": "FROGS_filter_OTU_contaminantSource",
                        "prefix": "",
                        "type": "radio",
                        "choices": [
                            {
                                "Don't apply this treatment": "no"
                            },
                            {
                                "Input a contaminant file": "history"
                            }
                        ],
                        "value": "no",
                        "label": "Chose where to find the list of contaminant OTU, either from your own fasta file, or from a database"
                    },
                    {
                        "name": "FROGS_filter_OTU_contaminantFile",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to your contaminant OTU fasta file"
                    },
                    {
                        "name": "FROGS_filter_OTU_contaminants_db",
                        "type": "select",
                        "choices": [
                            {
                                "Araport11": "\/contaminants\/Araport11-TAIR10Col0_Chl_MT\/Araport11-TAIR10Col0_Chl_MT.fa"
                            },
                            {
                                "phi": "\/contaminants\/phi\/phi.fa"
                            }
                        ],
                        "value": "\/contaminants\/Araport11-TAIR10Col0_Chl_MT\/Araport11-TAIR10Col0_Chl_MT.fa",
                        "label": "Contaminant database"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "frogs": [
                " Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 "
            ]
        },
        "yaml": "{\n  id: FROGS_filter_OTU,\n  name: FROGS filter OTU,\n  article: 10.1093\/bib\/bbab318,\n  website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n  git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n  description: \"Filters OTUs on several criteria\",\n  version: \"4.1.0\",\n  documentation: \"http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html\",\n  multiqc: \"generic_iframe\",\n  commands:\n    [\n      {\n        name: FROGS_filter_OTU,\n        command: \"cluster_filters.py\",\n        category: \"FROGS\",\n        output_dir: FROGS_filter_OTU,\n        inputs: \n          [\n            { name: sequence_file, type: \"fasta_file\", description: \"the sequences in fasta format\"},\n            { name: biom, type: \"biom\", description: \"The abundance of each OTU in each sample\"},\n            # { name: contaminant_file, type: \"contigs\", description: \"A sequence fasta file containing the reference sequence of known contaminant\"},\n          ],\n        outputs:\n          [\n            { name: \"filtered_sequences\", file: \"otuFilter_sequences.fasta\", type: \"fasta_file\", description: \"The sequences after filtering\"},\n            { name: \"abundance_file\", file: \"otuFilter_abundance.biom\", type: \"biom\", description: \"The abundance after filtering\"},\n            { name: \"excluded_file\", file: \"excluded.tsv\", type: \"tsv\", description: \"The list of the OTUs deleted by filters\"},\n            { name: \"summary\", file: \"filtOTU_report.html\", type: \"html\", description: \"The filters and the number of removed sequences\"}\n          ],\n        options:\n          [\n            {\n              name: FROGS_filter_OTU_threads,\n              prefix: -p,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: FROGS_filter_OTU_min_sample_presence,\n              prefix: ,\n              type: numeric,\n              value: 0,\n              min: 2,\n              max: NA,\n              step: NA,\n              label: \"Fill the field only if you want this treatment. Keep OTU if it is present in at least this number of samples.\",\n            },\n            {\n              name: FROGS_filter_OTU_min_abundance_proportion,\n              prefix: ,\n              type: numeric,\n              value: 0.00005,\n              min: 0,\n              max: 1,\n              step: NA,\n              label: \"Minimum proportion of sequences abundancy to keep OTU.\",\n            },\n            {\n              name: FROGS_filter_OTU_nb_biggest_otu,\n              prefix: ,\n              type: numeric,\n              value: 300,\n              min: 0,\n              max: NA,\n              step: NA,\n              label: \"Fill the fields only if you want this treatment. Keep the N biggest OTU\",\n            },\n            {\n              name: FROGS_filter_OTU_contaminantSource,\n              prefix: \"\",\n              type:  \"radio\",\n              choices:\n                [\n                  Don't apply this treatment: \"no\",\n                  Input a contaminant file: \"history\",\n                ],\n              value: \"no\",\n              label: \"Chose where to find the list of contaminant OTU, either from your own fasta file, or from a database\",\n            },\n            {\n              name: FROGS_filter_OTU_contaminantFile,\n              type: input_file,\n              value: \"\",\n              label: \"Path to your contaminant OTU fasta file\",\n            },\n            {\n              name: FROGS_filter_OTU_contaminants_db,\n              type: select,\n              choices: [\n                Araport11: \"\/contaminants\/Araport11-TAIR10Col0_Chl_MT\/Araport11-TAIR10Col0_Chl_MT.fa\",\n                phi: \"\/contaminants\/phi\/phi.fa\",\n              ],\n              value: \"\/contaminants\/Araport11-TAIR10Col0_Chl_MT\/Araport11-TAIR10Col0_Chl_MT.fa\",\n              label: \"Contaminant database\"\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # perl: [\n      #   \"sudo apt-get install python3 perl\" # deja install\u00e9\n      # ],\n      # frogs: [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget https:\/\/github.com\/geraldinepascal\/FROGS\/archive\/v4.1.0.tar.gz\",\n      #   \"tar -zxvf v4.1.0.tar.gz\",\n      #   \"cd FROGS-4.1.0\",\n      #   \"mkdir bin\"\n      # ],\n      # scipy: [\n      #   \"apt-get install python3-scipy\" # demande confirmation\n      # ],\n      # mbb_mqc_plugin:\n      # [\n      #   \"cd \/opt\/biotools\",\n      #   \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/mmassaviol\/mbb_mqc_plugin.git\",\n      #   \"cd mbb_mqc_plugin\",\n      #   \"python3 setup.py install\"\n      # ]\n    },\n  citations:  {\n    frogs: [\n      \" Maria Bernard, Olivier Ru\u00e9, Mahendra Mariadassou and G\u00e9raldine Pascal; FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers, Briefings in Bioinformatics 2021, 10.1093\/bib\/bbab318 \"\n    ]\n  }\n}\n"
    }
]