#!/usr/bin/env cwl-runner
###
# Copyright (c) 2021. Harvard University
#
# Developed by Research Software Engineering,
# Faculty of Arts and Sciences, Research Computing (FAS RC)
# Author: Michael A Bouzinier
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
cwlVersion: v1.2
class: CommandLineTool
baseCommand: [python, -m, gridmet.netCDF_components_consolidator]
requirements:
InlineJavascriptRequirement: {}
ResourceRequirement:
# coresMin: 1
coresMax: 4
outdirMin: 3072
doc: |
Given a NetCDF file with absolute values (e.g., for PM25) and a set of
NetCDF files containing percentage values for individual components,
this tool consolidates all data into a single NetCDF file with both
percentages and absolute values for all components.
inputs:
abs_values:
type: File[]
doc: "Path to downloaded file with absolute values"
inputBinding:
prefix: --input
components:
type: File[]
doc: "Paths to component files"
inputBinding:
prefix: --components
arguments:
- valueFrom: "."
prefix: --output
outputs:
log:
type: File?
outputBinding:
glob: "*.log"
consolidated_data:
type: File
outputBinding:
glob:
- "*.tif*"
- "**/*.tif*"
doc: |
The output NetCDF file, containing absolute values for the given
components
errors:
type: stderr
stderr: $("consolidate-" + inputs.abs_values.nameroot + ".err")