Mercurial > repos > shellac > sam_consensus_v3
comparison env/lib/python3.9/site-packages/cwltool/tests/wf/trick_revsort.cwl @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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-1:000000000000 | 0:4f3585e2f14b |
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1 #!/usr/bin/env cwl-runner | |
2 # | |
3 # This is a two-step workflow which uses "revtool" and "sorttool" defined above. | |
4 # | |
5 class: Workflow | |
6 doc: "Reverse the lines in a document, then sort those lines." | |
7 cwlVersion: v1.0 | |
8 | |
9 # Requirements & hints specify prerequisites and extensions to the workflow. | |
10 # In this example, DockerRequirement specifies a default Docker container | |
11 # in which the command line tools will execute. | |
12 hints: | |
13 - class: DockerRequirement | |
14 dockerPull: debian:8 | |
15 | |
16 | |
17 # The inputs array defines the structure of the input object that describes | |
18 # the inputs to the workflow. | |
19 # | |
20 # The "reverse_sort" input parameter demonstrates the "default" field. If the | |
21 # field "reverse_sort" is not provided in the input object, the default value will | |
22 # be used. | |
23 inputs: | |
24 workflow_input: | |
25 type: File | |
26 doc: "The input file to be processed." | |
27 format: iana:text/plain | |
28 default: | |
29 class: File | |
30 location: hello.txt | |
31 reverse_sort: | |
32 type: boolean | |
33 default: true | |
34 doc: "If true, reverse (decending) sort" | |
35 name: | |
36 type: string | |
37 doc: "Here to test for a bug in --pack" | |
38 | |
39 # The "outputs" array defines the structure of the output object that describes | |
40 # the outputs of the workflow. | |
41 # | |
42 # Each output field must be connected to the output of one of the workflow | |
43 # steps using the "outputSource" field. Here, the parameter "sorted_output" of the | |
44 # workflow comes from the "sorted_output" output of the "sorted" step. | |
45 outputs: | |
46 sorted_output: | |
47 type: File | |
48 outputSource: sorted/sorted_output | |
49 doc: "The output with the lines reversed and sorted." | |
50 | |
51 # The "steps" array lists the executable steps that make up the workflow. | |
52 # The tool to execute each step is listed in the "run" field. | |
53 # | |
54 # In the first step, the "in" field of the step connects the upstream | |
55 # parameter "workflow_input" of the workflow to the input parameter of the tool | |
56 # "revtool_input" | |
57 # | |
58 # In the second step, the "in" field of the step connects the output | |
59 # parameter "revtool_output" from the first step to the input parameter of the | |
60 # tool "sorted_input". | |
61 steps: | |
62 rev: | |
63 in: | |
64 revtool_input: workflow_input | |
65 out: [revtool_output] | |
66 run: revtool.cwl | |
67 | |
68 sorted: | |
69 in: | |
70 sorted_input: rev/revtool_output | |
71 reverse: reverse_sort | |
72 out: [sorted_output] | |
73 run: sorttool.cwl | |
74 | |
75 $namespaces: | |
76 iana: https://www.iana.org/assignments/media-types/ | |
77 | |
78 $schemas: | |
79 - empty2.ttl |