/
ocrevaluation-performance-test-files-wf-pack.cwl
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/
ocrevaluation-performance-test-files-wf-pack.cwl
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{
"cwlVersion": "v1.0",
"$graph": [
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"nlppln.commands.ls"
],
"doc": "List files in a directory.\n\nThis command can be used to convert a ``Directory`` into a list of files. This list can be filtered on file name by specifying ``--endswith``.\n",
"inputs": [
{
"type": [
"null",
"string"
],
"inputBinding": {
"prefix": "--endswith"
},
"id": "#ls.cwl/endswith"
},
{
"type": "Directory",
"inputBinding": {
"position": 2
},
"id": "#ls.cwl/in_dir"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "--recursive"
},
"id": "#ls.cwl/recursive"
}
],
"stdout": "cwl.output.json",
"outputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#ls.cwl/out_files"
}
],
"id": "#ls.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"nlppln.commands.merge_csv"
],
"requirements": [
{
"listing": "$(inputs.in_files)",
"class": "InitialWorkDirRequirement"
}
],
"arguments": [
{
"valueFrom": "$(runtime.outdir)",
"position": 1
}
],
"doc": "Merge csv files (with the same header) into a single csv file.",
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#merge-csv.cwl/in_files"
},
{
"type": [
"null",
"string"
],
"default": "merged.csv",
"inputBinding": {
"prefix": "--name=",
"separate": false
},
"id": "#merge-csv.cwl/name"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.name)"
},
"id": "#merge-csv.cwl/merged"
}
],
"id": "#merge-csv.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"ochre.ocrevaluation_extract"
],
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#ocrevaluation-extract.cwl/in_file"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*-character.csv"
},
"id": "#ocrevaluation-extract.cwl/character_data"
},
{
"type": "File",
"outputBinding": {
"glob": "*-global.csv"
},
"id": "#ocrevaluation-extract.cwl/global_data"
}
],
"id": "#ocrevaluation-extract.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "ScatterFeatureRequirement"
}
],
"inputs": [
{
"type": "Directory",
"id": "#ocrevaluation-performance-wf.cwl/gt"
},
{
"type": "Directory",
"id": "#ocrevaluation-performance-wf.cwl/ocr"
},
{
"default": "performance.csv",
"type": [
"null",
"string"
],
"id": "#ocrevaluation-performance-wf.cwl/out_name"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#ocrevaluation-performance-wf.cwl/merge-csv-1/merged",
"id": "#ocrevaluation-performance-wf.cwl/performance"
}
],
"steps": [
{
"run": "#ls.cwl",
"in": [
{
"source": "#ocrevaluation-performance-wf.cwl/ocr",
"id": "#ocrevaluation-performance-wf.cwl/ls-6/in_dir"
}
],
"out": [
"#ocrevaluation-performance-wf.cwl/ls-6/out_files"
],
"id": "#ocrevaluation-performance-wf.cwl/ls-6"
},
{
"run": "#ls.cwl",
"in": [
{
"source": "#ocrevaluation-performance-wf.cwl/gt",
"id": "#ocrevaluation-performance-wf.cwl/ls-7/in_dir"
}
],
"out": [
"#ocrevaluation-performance-wf.cwl/ls-7/out_files"
],
"id": "#ocrevaluation-performance-wf.cwl/ls-7"
},
{
"run": "#merge-csv.cwl",
"in": [
{
"source": "#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1/global_data",
"id": "#ocrevaluation-performance-wf.cwl/merge-csv-1/in_files"
},
{
"source": "#ocrevaluation-performance-wf.cwl/out_name",
"id": "#ocrevaluation-performance-wf.cwl/merge-csv-1/name"
}
],
"out": [
"#ocrevaluation-performance-wf.cwl/merge-csv-1/merged"
],
"id": "#ocrevaluation-performance-wf.cwl/merge-csv-1"
},
{
"run": "#ocrevaluation.cwl",
"in": [
{
"source": "#ocrevaluation-performance-wf.cwl/ls-7/out_files",
"id": "#ocrevaluation-performance-wf.cwl/ocrevaluation-1/gt"
},
{
"source": "#ocrevaluation-performance-wf.cwl/ls-6/out_files",
"id": "#ocrevaluation-performance-wf.cwl/ocrevaluation-1/ocr"
}
],
"out": [
"#ocrevaluation-performance-wf.cwl/ocrevaluation-1/out_file"
],
"scatter": [
"#ocrevaluation-performance-wf.cwl/ocrevaluation-1/gt",
"#ocrevaluation-performance-wf.cwl/ocrevaluation-1/ocr"
],
"scatterMethod": "dotproduct",
"id": "#ocrevaluation-performance-wf.cwl/ocrevaluation-1"
},
{
"run": "#ocrevaluation-extract.cwl",
"in": [
{
"source": "#ocrevaluation-performance-wf.cwl/ocrevaluation-1/out_file",
"id": "#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1/in_file"
}
],
"out": [
"#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1/character_data",
"#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1/global_data"
],
"scatter": [
"#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1/in_file"
],
"scatterMethod": "dotproduct",
"id": "#ocrevaluation-performance-wf.cwl/ocrevaluation-extract-1"
}
],
"id": "#ocrevaluation-performance-wf.cwl"
},
{
"class": "ExpressionTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"doc": "Save a list of files to a directory.\n",
"inputs": [
{
"type": "string",
"id": "#save-files-to-dir.cwl/dir_name"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#save-files-to-dir.cwl/in_files"
}
],
"outputs": [
{
"type": "Directory",
"id": "#save-files-to-dir.cwl/out"
}
],
"expression": "${\n return {\"out\": {\n \"class\": \"Directory\",\n \"basename\": inputs.dir_name,\n \"listing\": inputs.in_files\n } };\n}\n",
"id": "#save-files-to-dir.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"ochre.select_test_files"
],
"stdout": "cwl.output.json",
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 2
},
"id": "#select-test-files.cwl/datadivision"
},
{
"type": "Directory",
"inputBinding": {
"position": 1
},
"id": "#select-test-files.cwl/in_dir"
},
{
"type": [
"null",
"string"
],
"inputBinding": {
"prefix": "--name"
},
"id": "#select-test-files.cwl/name"
}
],
"outputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#select-test-files.cwl/out_files"
}
],
"id": "#select-test-files.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"inputs": [
{
"type": "File",
"id": "#main/datadivision"
},
{
"type": "Directory",
"id": "#main/gt"
},
{
"default": "gs",
"type": "string",
"id": "#main/gt_dir_name"
},
{
"type": "Directory",
"id": "#main/ocr"
},
{
"default": "ocr",
"type": "string",
"id": "#main/ocr_dir_name"
},
{
"default": "performance.csv",
"type": [
"null",
"string"
],
"id": "#main/out_name"
}
],
"outputs": [
{
"type": "File",
"outputSource": "#main/ocrevaluation-performance-wf/performance",
"id": "#main/performance"
}
],
"steps": [
{
"run": "#ocrevaluation-performance-wf.cwl",
"in": [
{
"source": "#main/save-files-to-dir/out",
"id": "#main/ocrevaluation-performance-wf/gt"
},
{
"source": "#main/save-files-to-dir-5/out",
"id": "#main/ocrevaluation-performance-wf/ocr"
}
],
"out": [
"#main/ocrevaluation-performance-wf/performance"
],
"id": "#main/ocrevaluation-performance-wf"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/gt_dir_name",
"id": "#main/save-files-to-dir/dir_name"
},
{
"source": "#main/select-test-files-1/out_files",
"id": "#main/save-files-to-dir/in_files"
}
],
"out": [
"#main/save-files-to-dir/out"
],
"id": "#main/save-files-to-dir"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/ocr_dir_name",
"id": "#main/save-files-to-dir-5/dir_name"
},
{
"source": "#main/select-test-files/out_files",
"id": "#main/save-files-to-dir-5/in_files"
}
],
"out": [
"#main/save-files-to-dir-5/out"
],
"id": "#main/save-files-to-dir-5"
},
{
"run": "#select-test-files.cwl",
"in": [
{
"source": "#main/datadivision",
"id": "#main/select-test-files/datadivision"
},
{
"source": "#main/ocr",
"id": "#main/select-test-files/in_dir"
}
],
"out": [
"#main/select-test-files/out_files"
],
"id": "#main/select-test-files"
},
{
"run": "#select-test-files.cwl",
"in": [
{
"source": "#main/datadivision",
"id": "#main/select-test-files-1/datadivision"
},
{
"source": "#main/gt",
"id": "#main/select-test-files-1/in_dir"
}
],
"out": [
"#main/select-test-files-1/out_files"
],
"id": "#main/select-test-files-1"
}
],
"id": "#main"
},
{
"class": "CommandLineTool",
"baseCommand": [
"java",
"-cp",
"/ocrevalUAtion/target/ocrevaluation.jar",
"eu.digitisation.Main"
],
"requirements": [
{
"class": "DockerRequirement",
"dockerPull": "nlppln/ocrevaluation-docker"
}
],
"arguments": [
{
"prefix": "-o",
"valueFrom": "$(runtime.outdir)/$(inputs.gt.nameroot)_out.html"
}
],
"inputs": [
{
"type": [
"null",
"string"
],
"inputBinding": {
"prefix": "-e"
},
"id": "#ocrevaluation.cwl/encoding"
},
{
"type": "File",
"inputBinding": {
"prefix": "-gt"
},
"id": "#ocrevaluation.cwl/gt"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "-ic"
},
"id": "#ocrevaluation.cwl/ignore_case"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "-id"
},
"id": "#ocrevaluation.cwl/ignore_diacritics"
},
{
"type": [
"null",
"boolean"
],
"inputBinding": {
"prefix": "-ip"
},
"id": "#ocrevaluation.cwl/ignore_punctuation"
},
{
"type": "File",
"inputBinding": {
"prefix": "-ocr"
},
"id": "#ocrevaluation.cwl/ocr"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.gt.nameroot)_out.html"
},
"id": "#ocrevaluation.cwl/out_file"
}
],
"id": "#ocrevaluation.cwl"
}
]
}