@apollo-annotation/apollo-cli - npm Package Compare versions

Comparing version 0.1.7 to 0.1.8

oclif.manifest.json

@@ -702,2 +702,57 @@ {
     },
+    "refseq:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
+      "examples": [
+        {
+          "description": "All sequences in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Only sequences for these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:get",
+      "pluginAlias": "@apollo-annotation/apollo-cli",
+      "pluginName": "@apollo-annotation/apollo-cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get reference sequences",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "get.js"
+      ]
+    },
     "feature:add-child": {
@@ -1509,57 +1564,2 @@ "aliases": [],
     },
-    "refseq:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
-      "examples": [
-        {
-          "description": "All sequences in the database:",
-          "command": "<%= config.bin %> <%= command.id %>"
-        },
-        {
-          "description": "Only sequences for these assemblies:",
-          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "refseq:get",
-      "pluginAlias": "@apollo-annotation/apollo-cli",
-      "pluginName": "@apollo-annotation/apollo-cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get reference sequences",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "refseq",
-        "get.js"
-      ]
-    },
     "user:get": {
@@ -1633,3 +1633,3 @@ "aliases": [],
   },
-  "version": "0.1.7"
+  "version": "0.1.8"
 }

package.json

 {
   "name": "@apollo-annotation/apollo-cli",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.7",
+  "version": "0.1.8",
   "author": "Apollo Team",
@@ -6,0 +6,0 @@ "repository": {

README.md

@@ -17,3 +17,3 @@ # Table of contents
 $ apollo (--version)
-@apollo-annotation/apollo-cli/0.1.7 linux-x64 node-v18.20.3
+@apollo-annotation/apollo-cli/0.1.8 linux-x64 node-v18.20.3
 $ apollo --help [COMMAND]
@@ -86,3 +86,3 @@ USAGE
 
-_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
+_See code: [src/commands/assembly/add-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/add-fasta.ts)_
 
@@ -121,3 +121,3 @@ ## `apollo assembly add-gff`
 
-_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
+_See code: [src/commands/assembly/add-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/add-gff.ts)_
 
@@ -164,3 +164,3 @@ ## `apollo assembly check`
 
-_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/check.ts)_
+_See code: [src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/check.ts)_
 
@@ -192,3 +192,3 @@ ## `apollo assembly delete`
 
-_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/delete.ts)_
+_See code: [src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/delete.ts)_
 
@@ -214,3 +214,3 @@ ## `apollo assembly get`
 
-_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/get.ts)_
+_See code: [src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/get.ts)_
 
@@ -249,3 +249,3 @@ ## `apollo assembly sequence`
 
-_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/assembly/sequence.ts)_
+_See code: [src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/assembly/sequence.ts)_
 
@@ -274,3 +274,3 @@ ## `apollo change get`
 
-_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/change/get.ts)_
+_See code: [src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/change/get.ts)_
 
@@ -330,3 +330,3 @@ ## `apollo config [KEY] [VALUE]`
 
-_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/config.ts)_
+_See code: [src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/config.ts)_
 
@@ -361,3 +361,3 @@ ## `apollo feature add-child`
 
-_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/add-child.ts)_
+_See code: [src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/add-child.ts)_
 
@@ -395,3 +395,3 @@ ## `apollo feature check`
 
-_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/check.ts)_
+_See code: [src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/check.ts)_
 
@@ -427,3 +427,3 @@ ## `apollo feature copy`
 
-_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/copy.ts)_
+_See code: [src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/copy.ts)_
 
@@ -452,3 +452,3 @@ ## `apollo feature delete`
 
-_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/delete.ts)_
+_See code: [src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/delete.ts)_
 
@@ -495,3 +495,3 @@ ## `apollo feature edit`
 
-_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/edit.ts)_
+_See code: [src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/edit.ts)_
 
@@ -536,3 +536,3 @@ ## `apollo feature edit-attribute`
 
-_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
+_See code: [src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
 
@@ -571,3 +571,3 @@ ## `apollo feature edit-coords`
 
-_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
+_See code: [src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
 
@@ -595,3 +595,3 @@ ## `apollo feature edit-type`
 
-_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/edit-type.ts)_
+_See code: [src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/edit-type.ts)_
 
@@ -629,3 +629,3 @@ ## `apollo feature get`
 
-_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/get.ts)_
+_See code: [src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/get.ts)_
 
@@ -659,3 +659,3 @@ ## `apollo feature get-id`
 
-_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/get-id.ts)_
+_See code: [src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/get-id.ts)_
 
@@ -688,3 +688,3 @@ ## `apollo feature import`
 
-_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/import.ts)_
+_See code: [src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/import.ts)_
 
@@ -740,3 +740,3 @@ ## `apollo feature search`
 
-_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/feature/search.ts)_
+_See code: [src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/feature/search.ts)_
 
@@ -801,3 +801,3 @@ ## `apollo help [COMMANDS]`
 
-_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/login.ts)_
+_See code: [src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/login.ts)_
 
@@ -831,3 +831,3 @@ ## `apollo logout`
 
-_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/logout.ts)_
+_See code: [src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/logout.ts)_
 
@@ -864,3 +864,3 @@ ## `apollo refseq get`
 
-_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/refseq/get.ts)_
+_See code: [src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/refseq/get.ts)_
 
@@ -887,3 +887,3 @@ ## `apollo status`
 
-_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/status.ts)_
+_See code: [src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/status.ts)_
 
@@ -923,3 +923,3 @@ ## `apollo user get`
 
-_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.7/packages/apollo-cli/src/commands/user/get.ts)_
+_See code: [src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.1.8/packages/apollo-cli/src/commands/user/get.ts)_
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