Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/cwltool/extensions.yml @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 $base: http://commonwl.org/cwltool#
2 $namespaces:
3 cwl: "https://w3id.org/cwl/cwl#"
4 $graph:
5 - $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
6
7 - name: LoadListingRequirement
8 type: record
9 extends: cwl:ProcessRequirement
10 inVocab: false
11 fields:
12 class:
13 type: string
14 doc: "Always 'LoadListingRequirement'"
15 jsonldPredicate:
16 "_id": "@type"
17 "_type": "@vocab"
18 loadListing:
19 type:
20 - type: enum
21 name: LoadListingEnum
22 symbols: [no_listing, shallow_listing, deep_listing]
23
24 - name: InplaceUpdateRequirement
25 type: record
26 inVocab: false
27 extends: cwl:ProcessRequirement
28 fields:
29 class:
30 type: string
31 doc: "Always 'InplaceUpdateRequirement'"
32 jsonldPredicate:
33 "_id": "@type"
34 "_type": "@vocab"
35 inplaceUpdate:
36 type: boolean
37
38 - name: Secrets
39 type: record
40 inVocab: false
41 extends: cwl:ProcessRequirement
42 fields:
43 class:
44 type: string
45 doc: "Always 'Secrets'"
46 jsonldPredicate:
47 "_id": "@type"
48 "_type": "@vocab"
49 secrets:
50 type: string[]
51 doc: |
52 List one or more input parameters that are sensitive (such as passwords)
53 which will be deliberately obscured from logging.
54 jsonldPredicate:
55 "_type": "@id"
56 refScope: 0
57
58
59 - name: TimeLimit
60 type: record
61 inVocab: false
62 extends: cwl:ProcessRequirement
63 doc: |
64 Set an upper limit on the execution time of a CommandLineTool or
65 ExpressionTool. A tool execution which exceeds the time limit may
66 be preemptively terminated and considered failed. May also be
67 used by batch systems to make scheduling decisions.
68 fields:
69 - name: class
70 type: string
71 doc: "Always 'TimeLimit'"
72 jsonldPredicate:
73 "_id": "@type"
74 "_type": "@vocab"
75 - name: timelimit
76 type: [long, string]
77 doc: |
78 The time limit, in seconds. A time limit of zero means no
79 time limit. Negative time limits are an error.
80
81
82 - name: WorkReuse
83 type: record
84 inVocab: false
85 extends: cwl:ProcessRequirement
86 doc: |
87 For implementations that support reusing output from past work (on
88 the assumption that same code and same input produce same
89 results), control whether to enable or disable the reuse behavior
90 for a particular tool or step (to accomodate situations where that
91 assumption is incorrect). A reused step is not executed but
92 instead returns the same output as the original execution.
93
94 If `enableReuse` is not specified, correct tools should assume it
95 is enabled by default.
96 fields:
97 - name: class
98 type: string
99 doc: "Always 'WorkReuse'"
100 jsonldPredicate:
101 "_id": "@type"
102 "_type": "@vocab"
103 - name: enableReuse
104 type: [boolean, string]
105 #default: true
106
107
108 - name: NetworkAccess
109 type: record
110 inVocab: false
111 extends: cwl:ProcessRequirement
112 doc: |
113 Indicate whether a process requires outgoing IPv4/IPv6 network
114 access. Choice of IPv4 or IPv6 is implementation and site
115 specific, correct tools must support both.
116
117 If `networkAccess` is false or not specified, tools must not
118 assume network access, except for localhost (the loopback device).
119
120 If `networkAccess` is true, the tool must be able to make outgoing
121 connections to network resources. Resources may be on a private
122 subnet or the public Internet. However, implementations and sites
123 may apply their own security policies to restrict what is
124 accessible by the tool.
125
126 Enabling network access does not imply a publically routable IP
127 address or the ability to accept inbound connections.
128
129 fields:
130 - name: class
131 type: string
132 doc: "Always 'NetworkAccess'"
133 jsonldPredicate:
134 "_id": "@type"
135 "_type": "@vocab"
136 - name: networkAccess
137 type: [boolean, string]
138
139 - name: ProcessGenerator
140 type: record
141 inVocab: true
142 extends: cwl:Process
143 documentRoot: true
144 fields:
145 - name: class
146 jsonldPredicate:
147 "_id": "@type"
148 "_type": "@vocab"
149 type: string
150 - name: run
151 type: [string, cwl:Process]
152 jsonldPredicate:
153 _id: "cwl:run"
154 _type: "@id"
155 doc: |
156 Specifies the process to run.