1#!/usr/bin/env cwl-runner
2###
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, -mdorieh.rasters.netCDF_components_consolidator]
25
26requirements:
27 InlineJavascriptRequirement: {}
28 ResourceRequirement:
29 # coresMin: 1
30 coresMax: 4
31 outdirMin: 3072
32
33
34doc: |
35 Given a NetCDF file with absolute values (e.g., for PM25) and a set of
36 NetCDF files containing percentage values for individual components,
37 this tool consolidates all data into a single NetCDF file with both
38 percentages and absolute values for all components.
39
40inputs:
41 abs_values:
42 type: File[]
43 doc: "Path to downloaded file with absolute values"
44 inputBinding:
45 prefix: --input
46 components:
47 type: File[]
48 doc: "Paths to component files"
49 inputBinding:
50 prefix: --components
51
52arguments:
53 - valueFrom: "."
54 prefix: --output
55
56outputs:
57 log:
58 type: File?
59 outputBinding:
60 glob: "*.log"
61 consolidated_data:
62 type: File
63 outputBinding:
64 glob:
65 - "*.tif*"
66 - "**/*.tif*"
67 doc: |
68 The output NetCDF file, containing absolute values for the given
69 components
70 errors:
71 type: stderr
72
73stderr: $("consolidate-" + inputs.abs_values.nameroot + ".err")