medicare_combine_tables.cwl

 1#!/usr/bin/env cwl-runner
 2### Medicare raw data federation tool
 3#  Copyright (c) 2021. Harvard University
 4#
 5#  Developed by Research Software Engineering,
 6#  Faculty of Arts and Sciences, Research Computing (FAS RC)
 7#  Author: Michael A Bouzinier
 8#
 9#  Licensed under the Apache License, Version 2.0 (the "License");
10#  you may not use this file except in compliance with the License.
11#  You may obtain a copy of the License at
12#
13#         http://www.apache.org/licenses/LICENSE-2.0
14#
15#  Unless required by applicable law or agreed to in writing, software
16#  distributed under the License is distributed on an "AS IS" BASIS,
17#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
18#  See the License for the specific language governing permissions and
19#  limitations under the License.
20#
21
22cwlVersion: v1.2
23class: CommandLineTool
24baseCommand: [python, -m, dorieh.cms.tools.mcr_combine_tables]
25
26requirements:
27  NetworkAccess:
28    networkAccess: True
29
30doc: |
31  This tool combines disparate tables with raw Medicare data into a single
32  view, transforming common columns to uniform type and format
33
34
35inputs:
36  database:
37    type: File
38    doc: Path to database connection file, usually database.ini
39    inputBinding:
40      prefix: --db
41  connection_name:
42    type: string
43    doc: The name of the section in the database.ini file
44    inputBinding:
45      prefix: --connection
46  table:
47    type: string
48    doc: the name of the table to be created
49    inputBinding:
50      prefix: --table
51  depends_on:
52    type: File?
53    doc: a special field used to enforce dependencies and execution order
54
55outputs:
56  log:
57    type: File
58    outputBinding:
59      glob: "*.log"
60  errors:
61    type: stderr
62
63stderr: mcr_combine_tables.err