miga-base 1.2.15.2 → 1.2.15.3

data/utils/enveomics/Manifest/Tasks/remote.json

@@ -1,355 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "BlastTab.kegg_pep2path_rest.pl",
-      "description": ["Takes a BLAST against KEGG_PEP (or KO) and retrieves",
-        "the pathways in which the subject peptides are involved."],
-      "requires": [
-        { "perl_lib": "JSON" },
-        { "perl_lib": "LWP::Simple" }
-      ],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "blast.txt",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input tabular BLAST file."
-        },
-        {
-          "name": "Cache file",
-          "arg": "out_file",
-          "description": ["(optional) File containing the saved cache. If",
-            "unset, the cache won't be recoverable across instances of this",
-            "script. It is strongly recommended to set a file. Multiple",
-            "parallel instances of this script may use the same cache file."]
-        },
-        ">",
-        {
-          "name": "output.txt",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited output file, with the columns: (1)",
-            "Query ID, (2) Subject ID, (3) Pathway ID, (4) Pathway (reference)",
-            "description, (5) Organism."]
-        }
-      ]
-    },
-    {
-      "task": "M5nr.getSequences.rb",
-      "description": ["Downloads a set of sequences from M5nr with a given",
-        "functional annotation."],
-      "help_arg": "--help",
-      "requires": [
-        { "ruby_gem": "restclient" },
-        { "ruby_gem": "open-uri" },
-        { "ruby_gem": "JSON" }
-      ],
-      "options": [
-        {
-          "opt": "--function",
-          "arg": "string",
-          "mandatory": true,
-          "description": "Functional annotation."
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "File containing the sequences."
-        },
-        {
-          "opt": "--max",
-          "arg": "integer",
-          "default": 0,
-          "description": ["Maximum number of sequences to download. Set to",
-            "0 to download all."]
-        },
-        {
-          "opt": "--recover",
-          "description": "If set, tries to recover a previous FastA."
-        },
-        {
-          "name": "URL",
-          "opt": "--url",
-          "arg": "string",
-          "default": "http://api.metagenomics.anl.gov/m5nr",
-          "description": "URL for M5nr API."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "EBIseq2tax.rb",
-      "description": ["Maps a list of EBI-supported IDs to their corresponding",
-        "NCBI taxonomy using EBI RESTful API."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits requests to EBI and NCBI servers."],
-      "requires": [
-        { "ruby_gem": "nokogiri" }
-      ],
-      "see_also": ["NCBIacc2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "IDs",
-          "opt": "--ids",
-          "arg": "string",
-          "description": "Comma-separated list of EBI IDs.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of EBI IDs,",
-            "one per line."],
-          "note": "Required unless 'IDs' is passed."
-        },
-        {
-          "opt": "--database",
-          "arg": "string",
-          "default": "uniprotkb",
-          "description": "EBI database defining the EBI IDs."
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Comma-delimited list of taxonomic ranks to report.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "opt": "--noheader",
-          "description": "Do not includ a header in the output."
-        },
-        {
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        }
-      ]
-    },
-    {
-      "task": "RefSeq.download.bash",
-      "description": ["Downloads a collection of sequences and/or annotations",
-        "from NCBI's RefSeq."],
-      "help_arg": "",
-      "requires": [
-        {
-          "description": "curl",
-          "test": "curl --version"
-        }
-      ],
-      "options": [
-        {
-          "name": "Organism",
-          "arg": "string",
-          "mandatory": true,
-          "description": ["The organism to download (e.g.,",
-            "Streptococcus_pneumoniae)."]
-        },
-        {
-          "name": "Extension",
-          "arg": "string",
-          "mandatory": true,
-          "default": ".*.gz",
-          "description": ["Extension to download. Common extensions include",
-            ".fna.gz (genomic sequences), .faa.gz (protein sequences),",
-            ".gff.gz (annotations), and .*.gz (all data)."]
-        },
-        {
-          "name": "Level",
-          "arg": "string",
-          "mandatory": true,
-          "default": "Any",
-          "description": ["Use only genomes with this assembly level. Common",
-            "levels are 'Complete Genome' and 'Contig'. By default, any",
-            "assembly level is allowed ('Any')."]
-        },
-        {
-          "name": "Directory",
-          "arg": "out_dir",
-          "description": ["Directory where the files are to be downladed.",
-            "By default, same as 'Organism'."]
-        }
-      ]
-    },
-    {
-      "task": "SRA.download.bash",
-      "description": ["Downloads the set of runs from a project, sample, or",
-        "experiment in SRA."],
-      "help_arg": "",
-      "requires": [
-        {
-          "description": "curl",
-          "test": "curl --version"
-        }
-      ],
-      "options": [
-        {
-          "name": "SRA ID",
-          "arg": "string",
-          "mandatory": true,
-          "description": "ID of the SRA Project, Sample, or Experiment."
-        },
-        {
-          "name": "dir",
-          "arg": "out_dir",
-          "description": ["Directory where the files are to be downladed. By",
-            "default, same as 'SRA ID'."]
-        }
-      ]
-    },
-    {
-      "task": "gi2tax.rb",
-      "description": ["Maps a list of NCBI GIs to their corresponding taxonomy",
-        "using the NCBI EUtilities."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits two requests to NCBI's servers.",
-        "*IMPORTANT NOTE*: NCBI is phasing out support for GIs. Please use",
-        "acc.ver instead with NCBIacc2tax.rb."],
-      "requires": [
-        { "ruby_gem": "nokogiri" },
-        { "ruby_gem": "json" }
-      ],
-      "see_also": ["NCBIacc2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "GIs",
-          "opt": "--gis",
-          "arg": "string",
-          "description": "Comma-separated list of GIs.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of GIs, one per",
-            "line."],
-          "note": "Required unless 'GIs' is passed."
-        },
-        {
-          "opt": "--protein",
-          "description": ["Use if the GIs are proteins. Otherwise, GIs are",
-            "assumed to be from the Nuccore Database."]
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Taxonomic ranks to report, separated by commas.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "name": "No header",
-          "opt": "--noheader",
-          "description": "Do not include a header in the output."
-        },
-        {
-          "name": "Tax IDs",
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "name": "Exact GI",
-          "opt": "--exact-gi",
-          "description": ["Returns only taxonomy associated with the exact GI",
-            "passed. By default, it attempts to update accession versions if",
-            "possible."]
-        },
-        {
-          "opt": "--ignore-missing",
-          "description": ["Does not report missing GIs in the output file. By",
-            "default, it reports GI and empty values for all other columns."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited table with GIs and taxonomic",
-            "classification."]
-        }
-      ]
-    },
-    {
-      "task": "NCBIacc2tax.rb",
-      "description": ["Maps a list of NCBI accessions to their corresponding",
-        "taxonomy using the NCBI EUtilities."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits two requests to NCBI's servers."],
-      "requires": [
-        { "ruby_gem": "nokogiri" },
-        { "ruby_gem": "json" }
-      ],
-      "see_also": ["EBIseq2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Accessions",
-          "opt": "--acc",
-          "arg": "string",
-          "description": "Comma-separated list of accessions.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of accessions,",
-            "one per line."],
-          "note": "Required unless 'Accessions' is passed."
-        },
-        {
-          "opt": "--protein",
-          "description": ["Use if the accessions are proteins. Otherwise,",
-            "accessions are assumed to be from the Nuccore Database."]
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Taxonomic ranks to report, separated by commas.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "name": "No header",
-          "opt": "--noheader",
-          "description": "Do not include a header in the output."
-        },
-        {
-          "name": "Tax IDs",
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "opt": "--ignore-missing",
-          "description": ["Does not report missing accessions in the output",
-            "file. By default, it reports GI and empty values for all other",
-            "columns."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited table with accessions and taxonomic",
-            "classification."]
-        }
-      ]
-    }
-  ]
-}