[
    {
        "id": "FROGS_phyloseq_stats",
        "name": "FROGS phyloseq_stats",
        "article": "10.1093\/bib\/bbab318",
        "website": "http:\/\/frogs.toulouse.inrae.fr\/",
        "git": "https:\/\/github.com\/geraldinepascal\/FROGS",
        "description": "Phyloseq to analyse abundance, diversity and structure",
        "version": "4.1.0",
        "documentation": "http:\/\/frogs.toulouse.inrae.fr\/html\/commands_utax.html",
        "multiqc": "generic_iframe",
        "commands": [
            {
                "name": "FROGS_phyloseq_stats",
                "cname": "FROGS_phyloseq_stats",
                "command": "",
                "category": "FROGS",
                "output_dir": "FROGS_phyloseq_stats",
                "inputs": [
                    {
                        "name": "biom_file",
                        "type": "biom",
                        "description": "The biom file contains the  OTU's informations: abundance and taxonomy."
                    },
                    {
                        "name": "otu_sequence_file",
                        "type": "fasta_file",
                        "description": "OTU sequences in fasta format"
                    },
                    {
                        "name": "popmap_file",
                        "type": "popmap",
                        "file": "",
                        "description": "Path to tsv file with metatdata of samples conditions"
                    }
                ],
                "outputs": [
                    {
                        "name": "alpha_div",
                        "file": "phyloseq_alpha_diversity.tsv.tsv",
                        "type": "tsv",
                        "description": "detailed alpha diversity indices in each sample"
                    },
                    {
                        "name": "wunifrac_div",
                        "file": "wunifrac.tsv",
                        "type": "tsv",
                        "description": "wunifrac distance matrix between samples"
                    }
                ],
                "options": [
                    {
                        "name": "FROGS_phyloseq_stats_varExp",
                        "type": "text",
                        "prefix": "--varExp",
                        "value": "",
                        "label": "The experiment variable that you want to analyse (column name in metadata file)."
                    }
                ]
            }
        ],
        "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 "
            ],
            "phyloseq": [
                "McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217"
            ]
        },
        "yaml": "{\n  id: FROGS_phyloseq_stats,\n  name: FROGS phyloseq_stats,\n  article: 10.1093\/bib\/bbab318,\n  website: \"http:\/\/frogs.toulouse.inrae.fr\/\",\n  git: \"https:\/\/github.com\/geraldinepascal\/FROGS\",\n  description: \"Phyloseq to analyse abundance, diversity and structure\",\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_phyloseq_stats,\n        cname: FROGS_phyloseq_stats,\n        command: \"\",\n        category: \"FROGS\",\n        output_dir: FROGS_phyloseq_stats,\n        inputs: \n          [\n            { name: \"biom_file\", type: \"biom\", description: \"The biom file contains the  OTU's informations: abundance and taxonomy.\" },\n            { name: \"otu_sequence_file\", type: \"fasta_file\", description: \"OTU sequences in fasta format\" },\n            { name: popmap_file, type: \"popmap\", file: \"\", description: \"Path to tsv file with metatdata of samples conditions\"},\n          ],\n        outputs:\n          [\n            { name: \"alpha_div\", file: \"phyloseq_alpha_diversity.tsv.tsv\", type: \"tsv\", description: \"detailed alpha diversity indices in each sample\"},\n            { name: \"wunifrac_div\", file: \"wunifrac.tsv\", type: \"tsv\", description: \"wunifrac distance matrix between samples\"},\n          ],\n        options:\n          [\n            { \n              name: \"FROGS_phyloseq_stats_varExp\", \n              type: \"text\", \n              prefix: \"--varExp\",\n              value: \"\",\n              label: \"The experiment variable that you want to analyse (column name in metadata file).\"\n            }\n          ],\n      },\n    ],  \n  install:\n    {\n      # perl: [\n      #   \"sudo apt-get install python3 perl\" # deja install\u00e9\n      # ],\n      # mafft: [\n      #   \"cd \/opt\/biotools\/\",\n      #   \"wget https:\/\/mafft.cbrc.jp\/alignment\/software\/mafft_7.471-1_amd64.deb\",\n      #   \"dpkg -i mafft_7.471-1_amd64.deb\",\n      #   \"rm mafft_7.471-1_amd64.deb\"\n      # ],\n      # FastTree: [\n      # \"cd \/opt\/biotools\",\n      # \"mkdir Fasttree && cd Fasttree\",\n      # \"wget http:\/\/www.microbesonline.org\/fasttree\/FastTree # this may change the version!\",\n      # \"chmod 777 FastTree\",\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      # post_frogs_install: [\n      #   \"mafftbin=$(which mafft)\", \n      #   \"ln -s $mafftbin \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\",\n      #   \"ln -s \/opt\/biotools\/Fasttree\/FastTree \/opt\/biotools\/FROGS-4.1.0\/libexec\/.\"\n      # ],\n      # phyloseq: [\n      # \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"joey711\/phyloseq\\\");)'\"\n      # ],\n      # plotly: [ \"Rscript -e 'install.packages(\\\"plotly\\\")' \"],\n      # phangorn: [\"Rscript -e 'install.packages(\\\"phangorn\\\", dependencies = TRUE)' \"],\n      # others: [\"Rscript -e 'install.packages( c(\\\"optparse\\\",\\\"calibrate\\\",\\\"formattable\\\")) '\"],\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      # pandoc: [apt-get install -y pandoc],\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    phyloseq: [\n      \"McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217\"\n    ],\n  }\n}\n"
    }
]