COMMANDS.json

{
    "iris": {
        "group-names":  [
                {"group-name": "tree", "description": "Phylogenetic Trees & Alignments"}
            ]
    },
    "cli": {
        "commands": [
                {"file-spec": "scripts/tree-aln-to-html.pl",                      "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-compute-abundance-profile.pl",        "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-create-group-file.pl",                "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-create-url-map.pl",                   "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-filter-abundance-profile-column.pl",  "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-find-alignment-ids.pl",               "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-find-tree-ids.pl",                    "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-get-alignment.pl",                    "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-get-leaf-id-mapping.pl",              "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-get-leaf-nodes.pl",                   "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-get-tree.pl",                         "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-html-add-boxes.pl",                   "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-html-relabel-leaves.pl",              "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-normalize-abundance-profile.pl",      "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-relabel-node-names.pl",               "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-remove-nodes.pl",                     "lang":"perl",   "iris-group-name": "tree"},
                {"file-spec": "scripts/tree-to-html.pl",                          "lang":"perl",   "iris-group-name": "tree"}
            ],
        "deprecated-commands": [
            {
                    "deprecated-name": "tree-url",
                    "file-name": "scripts/tree-url.pl",
                    "lang":"perl",
                    "deploy-to-iris":false,
                    "new-command-name": "NONE",
                    "warning-mssg":"You should not have to change urls for the tree scripts."
            }
        ]
    }
}