/
kb-tss-preprocess-all.cwl
876 lines (876 loc) · 31.3 KB
/
kb-tss-preprocess-all.cwl
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{
"cwlVersion": "v1.0",
"$graph": [
{
"class": "Workflow",
"requirements": [
{
"class": "ScatterFeatureRequirement"
}
],
"inputs": [
{
"default": "merged_changes.csv",
"type": "string",
"id": "#align-texts-wf.cwl/align_c"
},
{
"default": "merged_metadata.csv",
"type": "string",
"id": "#align-texts-wf.cwl/align_m"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#align-texts-wf.cwl/gs"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#align-texts-wf.cwl/ocr"
}
],
"outputs": [
{
"type": {
"items": "File",
"type": "array"
},
"outputSource": "#align-texts-wf.cwl/char-align/out_file",
"id": "#align-texts-wf.cwl/alignments"
},
{
"type": "File",
"outputSource": "#align-texts-wf.cwl/merge-json-1/merged",
"id": "#align-texts-wf.cwl/changes"
},
{
"type": "File",
"outputSource": "#align-texts-wf.cwl/merge-json/merged",
"id": "#align-texts-wf.cwl/metadata"
}
],
"steps": [
{
"run": "#align.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/ocr",
"id": "#align-texts-wf.cwl/align/file1"
},
{
"source": "#align-texts-wf.cwl/gs",
"id": "#align-texts-wf.cwl/align/file2"
}
],
"out": [
"#align-texts-wf.cwl/align/changes",
"#align-texts-wf.cwl/align/metadata"
],
"scatter": [
"#align-texts-wf.cwl/align/file1",
"#align-texts-wf.cwl/align/file2"
],
"scatterMethod": "dotproduct",
"id": "#align-texts-wf.cwl/align"
},
{
"run": "#char-align.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/gs",
"id": "#align-texts-wf.cwl/char-align/gs_text"
},
{
"source": "#align-texts-wf.cwl/align/metadata",
"id": "#align-texts-wf.cwl/char-align/metadata"
},
{
"source": "#align-texts-wf.cwl/ocr",
"id": "#align-texts-wf.cwl/char-align/ocr_text"
}
],
"out": [
"#align-texts-wf.cwl/char-align/out_file"
],
"scatter": [
"#align-texts-wf.cwl/char-align/gs_text",
"#align-texts-wf.cwl/char-align/ocr_text",
"#align-texts-wf.cwl/char-align/metadata"
],
"scatterMethod": "dotproduct",
"id": "#align-texts-wf.cwl/char-align"
},
{
"run": "#merge-json.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/align/metadata",
"id": "#align-texts-wf.cwl/merge-json/in_files"
},
{
"source": "#align-texts-wf.cwl/align_m",
"id": "#align-texts-wf.cwl/merge-json/name"
}
],
"out": [
"#align-texts-wf.cwl/merge-json/merged"
],
"id": "#align-texts-wf.cwl/merge-json"
},
{
"run": "#merge-json.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/align/changes",
"id": "#align-texts-wf.cwl/merge-json-1/in_files"
},
{
"source": "#align-texts-wf.cwl/align_c",
"id": "#align-texts-wf.cwl/merge-json-1/name"
}
],
"out": [
"#align-texts-wf.cwl/merge-json-1/merged"
],
"id": "#align-texts-wf.cwl/merge-json-1"
}
],
"id": "#align-texts-wf.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"ochre.char_align"
],
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 2
},
"id": "#char-align.cwl/gs_text"
},
{
"type": "File",
"inputBinding": {
"position": 3
},
"id": "#char-align.cwl/metadata"
},
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#char-align.cwl/ocr_text"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*.json"
},
"id": "#char-align.cwl/out_file"
}
],
"id": "#char-align.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"ochre.kb_tss_concat_files"
],
"requirements": [
{
"listing": "$(inputs.in_files)",
"class": "InitialWorkDirRequirement"
}
],
"arguments": [
{
"valueFrom": "$(runtime.outdir)",
"position": 1
}
],
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#kb-tss-concat-files.cwl/in_files"
}
],
"outputs": [
{
"type": {
"type": "array",
"items": "File"
},
"outputBinding": {
"glob": "*.txt"
},
"id": "#kb-tss-concat-files.cwl/out_files"
}
],
"id": "#kb-tss-concat-files.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "ScatterFeatureRequirement"
}
],
"inputs": [
{
"default": [
"SP"
],
"type": {
"type": "array",
"items": "string"
},
"id": "#kb-tss-preprocess-single-dir.cwl/element"
},
{
"default": "alto.xml",
"type": "string",
"id": "#kb-tss-preprocess-single-dir.cwl/endswith"
},
{
"type": "Directory",
"id": "#kb-tss-preprocess-single-dir.cwl/in_dir"
},
{
"default": "alto",
"type": "string",
"id": "#kb-tss-preprocess-single-dir.cwl/in_fmt"
},
{
"default": "text",
"type": "string",
"id": "#kb-tss-preprocess-single-dir.cwl/out_fmt"
},
{
"default": true,
"type": "boolean",
"id": "#kb-tss-preprocess-single-dir.cwl/recursive"
}
],
"outputs": [
{
"type": {
"type": "array",
"items": "File"
},
"outputSource": "#kb-tss-preprocess-single-dir.cwl/kb-tss-concat-files/out_files",
"id": "#kb-tss-preprocess-single-dir.cwl/text_files"
}
],
"steps": [
{
"run": "#kb-tss-concat-files.cwl",
"in": [
{
"source": "#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/out_file",
"id": "#kb-tss-preprocess-single-dir.cwl/kb-tss-concat-files/in_files"
}
],
"out": [
"#kb-tss-preprocess-single-dir.cwl/kb-tss-concat-files/out_files"
],
"id": "#kb-tss-preprocess-single-dir.cwl/kb-tss-concat-files"
},
{
"run": "#ls.cwl",
"in": [
{
"source": "#kb-tss-preprocess-single-dir.cwl/endswith",
"id": "#kb-tss-preprocess-single-dir.cwl/ls/endswith"
},
{
"source": "#kb-tss-preprocess-single-dir.cwl/in_dir",
"id": "#kb-tss-preprocess-single-dir.cwl/ls/in_dir"
},
{
"source": "#kb-tss-preprocess-single-dir.cwl/recursive",
"id": "#kb-tss-preprocess-single-dir.cwl/ls/recursive"
}
],
"out": [
"#kb-tss-preprocess-single-dir.cwl/ls/out_files"
],
"id": "#kb-tss-preprocess-single-dir.cwl/ls"
},
{
"run": "#ocr-transform.cwl",
"in": [
{
"source": "#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1/out_file",
"id": "#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/in_file"
},
{
"source": "#kb-tss-preprocess-single-dir.cwl/in_fmt",
"id": "#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/in_fmt"
},
{
"source": "#kb-tss-preprocess-single-dir.cwl/out_fmt",
"id": "#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/out_fmt"
}
],
"out": [
"#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/out_file"
],
"scatter": [
"#kb-tss-preprocess-single-dir.cwl/ocr-transform-1/in_file"
],
"scatterMethod": "dotproduct",
"id": "#kb-tss-preprocess-single-dir.cwl/ocr-transform-1"
},
{
"run": "#remove-xml-elements.cwl",
"in": [
{
"source": "#kb-tss-preprocess-single-dir.cwl/element",
"id": "#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1/element"
},
{
"source": "#kb-tss-preprocess-single-dir.cwl/ls/out_files",
"id": "#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1/xml_file"
}
],
"out": [
"#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1/out_file"
],
"scatter": [
"#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1/xml_file"
],
"scatterMethod": "dotproduct",
"id": "#kb-tss-preprocess-single-dir.cwl/remove-xml-elements-1"
}
],
"id": "#kb-tss-preprocess-single-dir.cwl"
},
{
"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",
"ochre.merge_json"
],
"requirements": [
{
"listing": "$(inputs.in_files)",
"class": "InitialWorkDirRequirement"
}
],
"arguments": [
{
"valueFrom": "$(runtime.outdir)",
"position": 1
}
],
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#merge-json.cwl/in_files"
},
{
"type": [
"null",
"string"
],
"inputBinding": {
"prefix": "--name=",
"separate": false
},
"id": "#merge-json.cwl/name"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*.csv"
},
"id": "#merge-json.cwl/merged"
}
],
"id": "#merge-json.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": "ocr-transform",
"requirements": [
{
"class": "DockerRequirement",
"dockerPull": "ubma/ocr-fileformat"
},
{
"class": "InlineJavascriptRequirement"
}
],
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 3
},
"id": "#ocr-transform.cwl/in_file"
},
{
"type": "string",
"inputBinding": {
"position": 1
},
"id": "#ocr-transform.cwl/in_fmt"
},
{
"type": "string",
"inputBinding": {
"position": 2
},
"id": "#ocr-transform.cwl/out_fmt"
}
],
"stdout": "${\n var nameroot = inputs.in_file.nameroot;\n var ext = 'xml';\n if(inputs.out_fmt == 'text'){\n ext = 'txt';\n }\n return nameroot + '.' + ext;\n}\n",
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "$(inputs.in_file.nameroot).*"
},
"id": "#ocr-transform.cwl/out_file"
}
],
"id": "#ocr-transform.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"nlppln.commands.remove_xml_elements"
],
"doc": "Remove specified XML elements from XML file.\n",
"inputs": [
{
"type": {
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-e"
}
},
"id": "#remove-xml-elements.cwl/element"
},
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#remove-xml-elements.cwl/xml_file"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*.xml"
},
"id": "#remove-xml-elements.cwl/out_file"
}
],
"id": "#remove-xml-elements.cwl"
},
{
"class": "ExpressionTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"doc": "Save a list of files to a directory.\n",
"inputs": [
{
"type": "string",
"id": "#save-files-to-dir.cwl/dir_name"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#save-files-to-dir.cwl/in_files"
}
],
"outputs": [
{
"type": "Directory",
"id": "#save-files-to-dir.cwl/out"
}
],
"expression": "${\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": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"inputs": [
{
"default": "align-Karmac-Origineel",
"type": "string",
"id": "#main/karmac_aligned_name"
},
{
"type": "Directory",
"id": "#main/karmac_dir"
},
{
"default": "Karmac",
"type": "string",
"id": "#main/karmac_name"
},
{
"default": "Origineel",
"type": "string",
"id": "#main/original_name"
},
{
"type": "Directory",
"id": "#main/orignal_dir"
},
{
"default": "align-X-Cago-Origineel",
"type": "string",
"id": "#main/xcago_aligned_name"
},
{
"type": "Directory",
"id": "#main/xcago_dir"
},
{
"default": "X-Cago",
"type": "string",
"id": "#main/xcago_name"
}
],
"outputs": [
{
"type": "Directory",
"outputSource": "#main/save-files-to-dir-9/out",
"id": "#main/karmac"
},
{
"type": "Directory",
"outputSource": "#main/save-files-to-dir-12/out",
"id": "#main/karmac_align"
},
{
"type": "Directory",
"outputSource": "#main/save-files-to-dir-10/out",
"id": "#main/original"
},
{
"type": "Directory",
"outputSource": "#main/save-files-to-dir-11/out",
"id": "#main/xcago"
},
{
"type": "Directory",
"outputSource": "#main/save-files-to-dir-13/out",
"id": "#main/xcago_align"
}
],
"steps": [
{
"run": "#align-texts-wf.cwl",
"in": [
{
"source": "#main/kb-tss-preprocess-single-dir/text_files",
"id": "#main/align-texts-wf-1/gs"
},
{
"source": "#main/kb-tss-preprocess-single-dir-1/text_files",
"id": "#main/align-texts-wf-1/ocr"
}
],
"out": [
"#main/align-texts-wf-1/alignments",
"#main/align-texts-wf-1/changes",
"#main/align-texts-wf-1/metadata"
],
"id": "#main/align-texts-wf-1"
},
{
"run": "#align-texts-wf.cwl",
"in": [
{
"source": "#main/kb-tss-preprocess-single-dir-2/text_files",
"id": "#main/align-texts-wf-3/gs"
},
{
"source": "#main/kb-tss-preprocess-single-dir-1/text_files",
"id": "#main/align-texts-wf-3/ocr"
}
],
"out": [
"#main/align-texts-wf-3/alignments",
"#main/align-texts-wf-3/changes",
"#main/align-texts-wf-3/metadata"
],
"id": "#main/align-texts-wf-3"
},
{
"run": "#kb-tss-preprocess-single-dir.cwl",
"in": [
{
"source": "#main/karmac_dir",
"id": "#main/kb-tss-preprocess-single-dir/in_dir"
}
],
"out": [
"#main/kb-tss-preprocess-single-dir/text_files"
],
"id": "#main/kb-tss-preprocess-single-dir"
},
{
"run": "#kb-tss-preprocess-single-dir.cwl",
"in": [
{
"source": "#main/orignal_dir",
"id": "#main/kb-tss-preprocess-single-dir-1/in_dir"
}
],
"out": [
"#main/kb-tss-preprocess-single-dir-1/text_files"
],
"id": "#main/kb-tss-preprocess-single-dir-1"
},
{
"run": "#kb-tss-preprocess-single-dir.cwl",
"in": [
{
"source": "#main/xcago_dir",
"id": "#main/kb-tss-preprocess-single-dir-2/in_dir"
}
],
"out": [
"#main/kb-tss-preprocess-single-dir-2/text_files"
],
"id": "#main/kb-tss-preprocess-single-dir-2"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/original_name",
"id": "#main/save-files-to-dir-10/dir_name"
},
{
"source": "#main/kb-tss-preprocess-single-dir-1/text_files",
"id": "#main/save-files-to-dir-10/in_files"
}
],
"out": [
"#main/save-files-to-dir-10/out"
],
"id": "#main/save-files-to-dir-10"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/xcago_name",
"id": "#main/save-files-to-dir-11/dir_name"
},
{
"source": "#main/kb-tss-preprocess-single-dir-2/text_files",
"id": "#main/save-files-to-dir-11/in_files"
}
],
"out": [
"#main/save-files-to-dir-11/out"
],
"id": "#main/save-files-to-dir-11"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/karmac_aligned_name",
"id": "#main/save-files-to-dir-12/dir_name"
},
{
"source": "#main/align-texts-wf-1/alignments",
"id": "#main/save-files-to-dir-12/in_files"
}
],
"out": [
"#main/save-files-to-dir-12/out"
],
"id": "#main/save-files-to-dir-12"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/xcago_aligned_name",
"id": "#main/save-files-to-dir-13/dir_name"
},
{
"source": "#main/align-texts-wf-3/alignments",
"id": "#main/save-files-to-dir-13/in_files"
}
],
"out": [
"#main/save-files-to-dir-13/out"
],
"id": "#main/save-files-to-dir-13"
},
{
"run": "#save-files-to-dir.cwl",
"in": [
{
"source": "#main/karmac_name",
"id": "#main/save-files-to-dir-9/dir_name"
},
{
"source": "#main/kb-tss-preprocess-single-dir/text_files",
"id": "#main/save-files-to-dir-9/in_files"
}
],
"out": [
"#main/save-files-to-dir-9/out"
],
"id": "#main/save-files-to-dir-9"
}
],
"id": "#main"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"/align.py"
],
"hints": [
{
"class": "DockerRequirement",
"dockerPull": "nlppln/edlib-align:0.1.2"
}
],
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#align.cwl/file1"
},
{
"type": "File",
"inputBinding": {
"position": 2
},
"id": "#align.cwl/file2"
},
{
"type": [
"null",
"Directory"
],
"inputBinding": {
"prefix": "--out_dir=",
"separate": false
},
"id": "#align.cwl/out_dir"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*-changes.json"
},
"id": "#align.cwl/changes"
},
{
"type": "File",
"outputBinding": {
"glob": "*-metadata.json"
},
"id": "#align.cwl/metadata"
}
],
"id": "#align.cwl"
}
]
}