cmd

var BapiCmd = &cobra.Command{
	Use:   "api",
	Short: "Query bioinformatics website APIs.",
	Long:  `Query bioinformatics website APIs.`,
	Run: func(cmd *cobra.Command, args []string) {
		BapiCmdRunOptions(cmd)
	},
}

var BioToolsCmd = &cobra.Command{
	Use:   "biots",
	Short: "Query bio.tools website APIs.",
	Long:  `Query bio.tools website APIs. Detail see https://biotools.readthedocs.io/en/latest/api_reference.html`,
	Run: func(cmd *cobra.Command, args []string) {
		BioToolsCmdRunOptions(cmd, args)
	},
}

var CligovCmd = &cobra.Command{
	Use:   "cligov",
	Short: "Query clinicaltrials.gov website APIs.",
	Long:  `Query clinicaltrials.gov website APIs. Detail see https://clinicaltrials.gov/api/gui/ref/api_urls`,
	Run: func(cmd *cobra.Command, args []string) {
		CligovCmdRunOptions(cmd, args)
	},
}

var Covid19Cmd = &cobra.Command{
	Use:   "covid19",
	Short: "Query covid19api.com website APIs.",
	Long:  `Query covid19api.com website APIs. Detail see https://covid19api.com`,
	Run: func(cmd *cobra.Command, args []string) {
		Covid19CmdRunOptions(cmd, args)
	},
}

var CrossRefCmd = &cobra.Command{
	Use:   "crf",
	Short: "Query crossref guestquery APIs.",
	Long:  `Query crossref guestquery APIs. Detail see https://www.crossref.org/guestquery website.`,
	Run: func(cmd *cobra.Command, args []string) {
		CrossRefCmdRunOptions(cmd, args)
	},
}

var Dataset2toolsCmd = &cobra.Command{
	Use:   "dta",
	Short: "Query dataset2tools website APIs: datasets (d), tools (t), and canned analysis (a).",
	Long:  `Query dataset2tools website APIs: datasets (d), tools (t), and canned analysis (a).`,
	Run: func(cmd *cobra.Command, args []string) {
		Dataset2toolsCmdRunOptions(cmd, args)
	},
}

var GdcCmd = &cobra.Command{
	Use:   "gdc",
	Short: "Query GDC portal website APIs.",
	Long:  `Query GDC portal website APIs.`,
	Run: func(cmd *cobra.Command, args []string) {
		GdcCmdRunOptions(cmd, args)
	},
}

var MgRastAnnoCmd = &cobra.Command{
	Use:   "anno",
	Short: "Query http://api.mg-rast.org/anno website annotation APIs.",
	Long:  `Query http://api.mg-rast.org/anno website annotation APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		MgRastEndp.Annotation = true
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastCmd = &cobra.Command{
	Use:   "mgrast",
	Short: "Query mg-rast website APIs.",
	Long:  `Query mg-rast website APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastComputeCmd = &cobra.Command{
	Use:   "compute",
	Short: "Query http://api.mg-rast.org/compute website compute APIs.",
	Long:  `Query http://api.mg-rast.org/compute website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		MgRastEndp.Compute = true
		MgRastEndp.ParamsCompute.Retry = bapiClis.Retries
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastDarkMatterCmd = &cobra.Command{
	Use:   "darkmatter",
	Short: "Query http://api.mg-rast.org/darkmatter website compute APIs.",
	Long:  `Query http://api.mg-rast.org/darkmatter website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		MgRastEndp.DarkMatter = true
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastDownloadCmd = &cobra.Command{
	Use:   "download",
	Short: "Query http://api.mg-rast.org/download website compute APIs.",
	Long:  `Query http://api.mg-rast.org/download website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		MgRastEndp.Download = true
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastEndp types.MgRastEndpoints

var MgRastLibraryCmd = &cobra.Command{
	Use:   "library [id]",
	Short: "Query http://api.mg-rast.org/library website compute APIs.",
	Long:  `Query http://api.mg-rast.org/library website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		if len(args) > 0 {
			MgRastEndp.Library = args[0]
		} else {
			MgRastEndp.Library = "nil"
		}
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastProjectCmd = &cobra.Command{
	Use:   "proj",
	Short: "Query http://api.mg-rast.org/project website compute APIs.",
	Long:  `Query http://api.mg-rast.org/project website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		if len(args) > 0 {
			MgRastEndp.Project = args[0]
		} else {
			MgRastEndp.Project = "nil"
		}
		MgRastCmdRunOptions(cmd, args)
	},
}

var MgRastSampleCmd = &cobra.Command{
	Use:   "sample [id]",
	Short: "Query http://api.mg-rast.org/sample website compute APIs.",
	Long:  `Query http://api.mg-rast.org/sample website compute APIs. Detail see http://api.mg-rast.org/api.html`,
	Run: func(cmd *cobra.Command, args []string) {
		if len(args) > 0 {
			MgRastEndp.Sample = args[0]
		} else {
			MgRastEndp.Sample = "nil"
		}
		MgRastCmdRunOptions(cmd, args)
	},
}

var NcbiCmd = &cobra.Command{
	Use:   "ncbi",
	Short: "Query ncbi website APIs.",
	Long:  `Query ncbi website APIs.`,
	Run: func(cmd *cobra.Command, args []string) {
		NcbiCmdRunOptions(cmd, args)
	},
}