Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/cwltool/extensions.yml @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/cwltool/extensions.yml Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,156 @@ +$base: http://commonwl.org/cwltool# +$namespaces: + cwl: "https://w3id.org/cwl/cwl#" +$graph: +- $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml + +- name: LoadListingRequirement + type: record + extends: cwl:ProcessRequirement + inVocab: false + fields: + class: + type: string + doc: "Always 'LoadListingRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + loadListing: + type: + - type: enum + name: LoadListingEnum + symbols: [no_listing, shallow_listing, deep_listing] + +- name: InplaceUpdateRequirement + type: record + inVocab: false + extends: cwl:ProcessRequirement + fields: + class: + type: string + doc: "Always 'InplaceUpdateRequirement'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + inplaceUpdate: + type: boolean + +- name: Secrets + type: record + inVocab: false + extends: cwl:ProcessRequirement + fields: + class: + type: string + doc: "Always 'Secrets'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + secrets: + type: string[] + doc: | + List one or more input parameters that are sensitive (such as passwords) + which will be deliberately obscured from logging. + jsonldPredicate: + "_type": "@id" + refScope: 0 + + +- name: TimeLimit + type: record + inVocab: false + extends: cwl:ProcessRequirement + doc: | + Set an upper limit on the execution time of a CommandLineTool or + ExpressionTool. A tool execution which exceeds the time limit may + be preemptively terminated and considered failed. May also be + used by batch systems to make scheduling decisions. + fields: + - name: class + type: string + doc: "Always 'TimeLimit'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: timelimit + type: [long, string] + doc: | + The time limit, in seconds. A time limit of zero means no + time limit. Negative time limits are an error. + + +- name: WorkReuse + type: record + inVocab: false + extends: cwl:ProcessRequirement + doc: | + For implementations that support reusing output from past work (on + the assumption that same code and same input produce same + results), control whether to enable or disable the reuse behavior + for a particular tool or step (to accomodate situations where that + assumption is incorrect). A reused step is not executed but + instead returns the same output as the original execution. + + If `enableReuse` is not specified, correct tools should assume it + is enabled by default. + fields: + - name: class + type: string + doc: "Always 'WorkReuse'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: enableReuse + type: [boolean, string] + #default: true + + +- name: NetworkAccess + type: record + inVocab: false + extends: cwl:ProcessRequirement + doc: | + Indicate whether a process requires outgoing IPv4/IPv6 network + access. Choice of IPv4 or IPv6 is implementation and site + specific, correct tools must support both. + + If `networkAccess` is false or not specified, tools must not + assume network access, except for localhost (the loopback device). + + If `networkAccess` is true, the tool must be able to make outgoing + connections to network resources. Resources may be on a private + subnet or the public Internet. However, implementations and sites + may apply their own security policies to restrict what is + accessible by the tool. + + Enabling network access does not imply a publically routable IP + address or the ability to accept inbound connections. + + fields: + - name: class + type: string + doc: "Always 'NetworkAccess'" + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + - name: networkAccess + type: [boolean, string] + +- name: ProcessGenerator + type: record + inVocab: true + extends: cwl:Process + documentRoot: true + fields: + - name: class + jsonldPredicate: + "_id": "@type" + "_type": "@vocab" + type: string + - name: run + type: [string, cwl:Process] + jsonldPredicate: + _id: "cwl:run" + _type: "@id" + doc: | + Specifies the process to run.