[
    {
        "id": "FROGS_filter_affiliation",
        "name": "FROGS filter affiliation",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Filters OTUs on several affiliation criteria",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "generic_iframe",
        "commands": [
            {
                "name": "FROGS_filter_affiliation",
                "command": "affiliation_filters.py",
                "category": "FROGS",
                "output_dir": "FROGS_filter_affiliation",
                "inputs": [
                    {
                        "name": "fasta",
                        "type": "fasta_file",
                        "description": "The sequence file to filter"
                    },
                    {
                        "name": "biom",
                        "type": "biom",
                        "description": "The abundance file to filter"
                    }
                ],
                "outputs": [
                    {
                        "name": "biom_filtered",
                        "file": "affiFilter_abundance.biom",
                        "type": "biom",
                        "description": "the abundance file with filtered affiliation"
                    },
                    {
                        "name": "sequence_file",
                        "file": "affiFilter_sequences.fasta",
                        "type": "fasta_file",
                        "description": "the filtered sequences"
                    },
                    {
                        "name": "impacted",
                        "file": "impacted.tsv",
                        "type": "tsv",
                        "description": "The list of the OTUs deleted or hidden or with updated blast affiliation"
                    },
                    {
                        "name": "multihit",
                        "file": "impacted.multihit.tsv",
                        "type": "tsv",
                        "description": "The list of blast affiliations for multi-affiliated impacted OTU"
                    },
                    {
                        "name": "summary",
                        "file": "report_mqc.html",
                        "type": "html",
                        "description": "summary"
                    }
                ],
                "options": [
                    {
                        "name": "FROGS_filter_affiliation_mode",
                        "prefix": "",
                        "type": "radio",
                        "choices": [
                            {
                                "Deleting mode": "delete"
                            },
                            {
                                "Hidding mode": "mask"
                            }
                        ],
                        "value": "mask",
                        "label": "Do you want to delete OTU or hide affiliations?"
                    },
                    {
                        "name": "FROGS_filter_affiliation_max_blast_evalue",
                        "prefix": null,
                        "type": "numeric",
                        "value": "1e-15",
                        "min": 0,
                        "max": 1,
                        "step": "NA",
                        "label": "Maximum e-value"
                    },
                    {
                        "name": "FROGS_filter_affiliation_min_blast_identity",
                        "prefix": null,
                        "type": "numeric",
                        "value": 1,
                        "min": 0,
                        "max": 1,
                        "step": "NA",
                        "label": "Minimum identity"
                    },
                    {
                        "name": "FROGS_filter_affiliation_min_blast_coverage",
                        "prefix": null,
                        "type": "numeric",
                        "value": 1,
                        "min": 0,
                        "max": 1,
                        "step": "NA",
                        "label": "Minimum coverage"
                    },
                    {
                        "name": "FROGS_filter_affiliation_min_blast_length",
                        "prefix": null,
                        "type": "numeric",
                        "value": 150,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum alignment length"
                    },
                    {
                        "name": "FROGS_filter_affiliation_rdp",
                        "prefix": "--rdp",
                        "type": "checkbox",
                        "value": false,
                        "label": "Taxonomical rank on which to apply bootstrap filter"
                    },
                    {
                        "name": "FROGS_filter_affiliation_min_rdp_bootstrap",
                        "prefix": null,
                        "type": "numeric",
                        "value": 0.8,
                        "min": 0,
                        "max": 1,
                        "step": "NA",
                        "label": "Minimum bootstrap"
                    }
                ]
            }
        ],
        "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_affiliation,\n  name: FROGS filter affiliation,\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 affiliation 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_affiliation,\n        command: \"affiliation_filters.py\",\n        category: \"FROGS\",\n        output_dir: FROGS_filter_affiliation,\n        inputs: \n          [\n            { name: fasta, type: \"fasta_file\", description: \"The sequence file to filter\"},\n            { name: biom, type: \"biom\", description: \"The abundance file to filter\"},\n          ],\n        outputs:\n          [\n            { name: \"biom_filtered\", file: \"affiFilter_abundance.biom\", type: \"biom\", description: \"the abundance file with filtered affiliation\"},\n            #sequence file is produced only in delete mode\n            { name: \"sequence_file\", file: \"affiFilter_sequences.fasta\", type: \"fasta_file\", description: \"the filtered sequences\"},\n            { name: \"impacted\", file: \"impacted.tsv\", type: \"tsv\", description: \"The list of the OTUs deleted or hidden or with updated blast affiliation\"},\n            { name: \"multihit\", file: \"impacted.multihit.tsv\", type: \"tsv\", description: \"The list of blast affiliations for multi-affiliated impacted OTU\"},\n            { name: \"summary\", file: \"report_mqc.html\", type: \"html\", description: \"summary\"}\n          ],\n        options:\n          [\n            {\n              name: FROGS_filter_affiliation_mode,\n              prefix: \"\",\n              type:  \"radio\",\n              choices:\n                [\n                  Deleting mode: \"delete\",\n                  Hidding mode: \"mask\",\n                ],\n              value: \"mask\",\n              label: \"Do you want to delete OTU or hide affiliations?\",\n            },\n            {\n              name: FROGS_filter_affiliation_max_blast_evalue,\n              prefix: ,\n              type: numeric,\n              value: 1e-15,\n              min: 0,\n              max: 1.0,\n              step: NA,\n              label: \"Maximum e-value\",\n            },\n            {\n              name: FROGS_filter_affiliation_min_blast_identity,\n              prefix: ,\n              type: numeric,\n              value: 1,\n              min: 0.0,\n              max: 1.0,\n              step: NA,\n              label: \"Minimum identity\",\n            },\n            {\n              name: FROGS_filter_affiliation_min_blast_coverage,\n              prefix: ,\n              type: numeric,\n              value: 1,\n              min: 0.0,\n              max: 1.0,\n              step: NA,\n              label: \"Minimum coverage\",\n            },\n            {\n              name: FROGS_filter_affiliation_min_blast_length,\n              prefix: ,\n              type: numeric,\n              value: 150,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Minimum alignment length\",\n            },\n            {\n              name: FROGS_filter_affiliation_rdp,\n              prefix: --rdp,\n              type: checkbox,\n              value: False,\n              label: \"Taxonomical rank on which to apply bootstrap filter\",\n            },\n            {\n              name: FROGS_filter_affiliation_min_rdp_bootstrap,\n              prefix: ,\n              type: numeric,\n              value: 0.8,\n              min: 0,\n              max: 1,\n              step: NA,\n              label: \"Minimum bootstrap\",\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      # ncbi-blast-2.10.1: [\n      #   \"cd \/opt\/biotools\/\",\n      #   \"wget ftp:\/\/ftp.ncbi.nlm.nih.gov\/blast\/executables\/blast+\/2.10.1\/ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n      #   \"tar xvzf ncbi-blast-2.10.1+-x64-linux.tar.gz\",\n      # ],\n      # frogs_blast_post_install: [\n      #  # add blast to FROGS\n      #   \"ln -s \/opt\/biotools\/ncbi-blast-2.10.1+\/bin\/blastn \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\"\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"
    }
]