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sac-preprocess.cwl
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sac-preprocess.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-1/out_file",
"id": "#align-texts-wf.cwl/alignments"
},
{
"type": "File",
"outputSource": "#align-texts-wf.cwl/merge-json-5/merged",
"id": "#align-texts-wf.cwl/changes"
},
{
"type": "File",
"outputSource": "#align-texts-wf.cwl/merge-json-4/merged",
"id": "#align-texts-wf.cwl/metadata"
}
],
"steps": [
{
"run": "#align.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/ocr",
"id": "#align-texts-wf.cwl/align-1/file1"
},
{
"source": "#align-texts-wf.cwl/gs",
"id": "#align-texts-wf.cwl/align-1/file2"
}
],
"out": [
"#align-texts-wf.cwl/align-1/changes",
"#align-texts-wf.cwl/align-1/metadata"
],
"scatter": [
"#align-texts-wf.cwl/align-1/file1",
"#align-texts-wf.cwl/align-1/file2"
],
"scatterMethod": "dotproduct",
"id": "#align-texts-wf.cwl/align-1"
},
{
"run": "#char-align.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/gs",
"id": "#align-texts-wf.cwl/char-align-1/gs_text"
},
{
"source": "#align-texts-wf.cwl/align-1/metadata",
"id": "#align-texts-wf.cwl/char-align-1/metadata"
},
{
"source": "#align-texts-wf.cwl/ocr",
"id": "#align-texts-wf.cwl/char-align-1/ocr_text"
}
],
"out": [
"#align-texts-wf.cwl/char-align-1/out_file"
],
"scatter": [
"#align-texts-wf.cwl/char-align-1/gs_text",
"#align-texts-wf.cwl/char-align-1/ocr_text",
"#align-texts-wf.cwl/char-align-1/metadata"
],
"scatterMethod": "dotproduct",
"id": "#align-texts-wf.cwl/char-align-1"
},
{
"run": "#merge-json.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/align-1/metadata",
"id": "#align-texts-wf.cwl/merge-json-4/in_files"
},
{
"source": "#align-texts-wf.cwl/align_m",
"id": "#align-texts-wf.cwl/merge-json-4/name"
}
],
"out": [
"#align-texts-wf.cwl/merge-json-4/merged"
],
"id": "#align-texts-wf.cwl/merge-json-4"
},
{
"run": "#merge-json.cwl",
"in": [
{
"source": "#align-texts-wf.cwl/align-1/changes",
"id": "#align-texts-wf.cwl/merge-json-5/in_files"
},
{
"source": "#align-texts-wf.cwl/align_c",
"id": "#align-texts-wf.cwl/merge-json-5/name"
}
],
"out": [
"#align-texts-wf.cwl/merge-json-5/merged"
],
"id": "#align-texts-wf.cwl/merge-json-5"
}
],
"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.merge_json"
],
"requirements": [
{
"listing": "$(inputs.in_files)",
"class": "InitialWorkDirRequirement"
}
],
"arguments": [
{
"valueFrom": "$(runtime.outdir)",
"position": 1
}
],
"inputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#merge-json.cwl/in_files"
},
{
"type": [
"null",
"string"
],
"inputBinding": {
"prefix": "--name=",
"separate": false
},
"id": "#merge-json.cwl/name"
}
],
"outputs": [
{
"type": "File",
"outputBinding": {
"glob": "*.csv"
},
"id": "#merge-json.cwl/merged"
}
],
"id": "#merge-json.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"mkdir"
],
"doc": "Create directory",
"inputs": [
{
"type": "string",
"inputBinding": {
"position": 1
},
"id": "#mkdir.cwl/dir_name"
}
],
"outputs": [
{
"type": "Directory",
"outputBinding": {
"glob": "*"
},
"id": "#mkdir.cwl/out"
}
],
"id": "#mkdir.cwl"
},
{
"class": "CommandLineTool",
"baseCommand": [
"python",
"-m",
"ochre.sac2gs_and_ocr"
],
"inputs": [
{
"type": "Directory",
"inputBinding": {
"position": 1
},
"id": "#sac2gs-and-ocr.cwl/in_dir"
}
],
"stdout": "cwl.output.json",
"outputs": [
{
"type": {
"type": "array",
"items": "File"
},
"id": "#sac2gs-and-ocr.cwl/gs_de"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#sac2gs-and-ocr.cwl/gs_fr"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#sac2gs-and-ocr.cwl/ocr_de"
},
{
"type": {
"type": "array",
"items": "File"
},
"id": "#sac2gs-and-ocr.cwl/ocr_fr"
}
],
"id": "#sac2gs-and-ocr.cwl"
},
{
"class": "ExpressionTool",
"requirements": [
{
"class": "InlineJavascriptRequirement"
}
],
"doc": "Save a directory to a subdirectory.\n\nPuts ``inner_dir`` into the ``outer_dir``.\n",
"inputs": [
{
"type": "Directory",
"id": "#save-dir-to-subdir.cwl/inner_dir"
},
{
"type": "Directory",
"id": "#save-dir-to-subdir.cwl/outer_dir"
}
],
"outputs": [
{
"type": "Directory",
"id": "#save-dir-to-subdir.cwl/out"
}
],
"expression": "${\n return {\"out\": {\n \"class\": \"Directory\",\n \"basename\": inputs.outer_dir.basename + \"/\" + inputs.inner_dir.basename,\n \"listing\": inputs.inner_dir.listing\n } };\n}\n",
"id": "#save-dir-to-subdir.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": [
"tar",
"-xzf"
],
"doc": "Extract zipped tar archives.",
"inputs": [
{
"type": "File",
"inputBinding": {
"position": 1
},
"id": "#tar.cwl/in_file"
}
],
"outputs": [
{
"type": "Directory",
"outputBinding": {
"glob": "*"
},
"id": "#tar.cwl/out"
}
],
"id": "#tar.cwl"
},
{
"class": "Workflow",
"requirements": [
{
"class": "SubworkflowFeatureRequirement"
}
],
"inputs": [
{
"default": "align",
"type": "string",
"id": "#main/align_dir_name"
},
{
"type": "File",
"id": "#main/data_file"
},
{
"default": "de",
"type": "string",
"id": "#main/de_dir_name"
},
{
"default": "fr",
"type": "string",
"id": "#main/fr_dir_name"
},
{
"default": "gs",
"type": "string",
"id": "#main/gs_dir_name"
},
{
"default": "ocr",
"type": "string",
"id": "#main/ocr_dir_name"
}
],
"outputs": [
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-10/out",
"id": "#main/align_de"
},
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-11/out",
"id": "#main/align_fr"
},
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-7/out",
"id": "#main/gs_de"
},
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-9/out",
"id": "#main/gs_fr"
},
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-6/out",
"id": "#main/ocr_de"
},
{
"type": "Directory",
"outputSource": "#main/save-dir-to-subdir-8/out",
"id": "#main/ocr_fr"
}
],
"steps": [
{
"run": "#align-texts-wf.cwl",
"in": [
{
"source": "#main/sac2gs-and-ocr-1/gs_de",
"id": "#main/align-texts-wf-4/gs"
},
{
"source": "#main/sac2gs-and-ocr-1/ocr_de",
"id": "#main/align-texts-wf-4/ocr"
}
],
"out": [
"#main/align-texts-wf-4/alignments",
"#main/align-texts-wf-4/changes",
"#main/align-texts-wf-4/metadata"
],
"id": "#main/align-texts-wf-4"
},
{
"run": "#align-texts-wf.cwl",
"in": [
{
"source": "#main/sac2gs-and-ocr-1/gs_fr",
"id": "#main/align-texts-wf-5/gs"
},
{
"source": "#main/sac2gs-and-ocr-1/ocr_fr",
"id": "#main/align-texts-wf-5/ocr"
}
],
"out": [
"#main/align-texts-wf-5/alignments",
"#main/align-texts-wf-5/changes",
"#main/align-texts-wf-5/metadata"
],
"id": "#main/align-texts-wf-5"
},
{
"run": "#mkdir.cwl",
"in": [
{
"source": "#main/de_dir_name",
"id": "#main/mkdir-2/dir_name"
}
],
"out": [
"#main/mkdir-2/out"
],
"id": "#main/mkdir-2"
},
{
"run": "#mkdir.cwl",
"in": [
{
"source": "#main/fr_dir_name",
"id": "#main/mkdir-3/dir_name"
}
],
"out": [
"#main/mkdir-3/out"
],
"id": "#main/mkdir-3"
},
{
"run": "#sac2gs-and-ocr.cwl",
"in": [
{
"source": "#main/tar-1/out",
"id": "#main/sac2gs-and-ocr-1/in_dir"
}
],
"out": [
"#main/sac2gs-and-ocr-1/gs_de",
"#main/sac2gs-and-ocr-1/gs_fr",
"#main/sac2gs-and-ocr-1/ocr_de",
"#main/sac2gs-and-ocr-1/ocr_fr"
],
"id": "#main/sac2gs-and-ocr-1"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-19/out",
"id": "#main/save-dir-to-subdir-10/inner_dir"
},
{
"source": "#main/mkdir-2/out",
"id": "#main/save-dir-to-subdir-10/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-10/out"
],
"id": "#main/save-dir-to-subdir-10"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-20/out",
"id": "#main/save-dir-to-subdir-11/inner_dir"
},
{
"source": "#main/mkdir-3/out",
"id": "#main/save-dir-to-subdir-11/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-11/out"
],
"id": "#main/save-dir-to-subdir-11"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-15/out",
"id": "#main/save-dir-to-subdir-6/inner_dir"
},
{
"source": "#main/mkdir-2/out",
"id": "#main/save-dir-to-subdir-6/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-6/out"
],
"id": "#main/save-dir-to-subdir-6"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-16/out",
"id": "#main/save-dir-to-subdir-7/inner_dir"
},
{
"source": "#main/mkdir-2/out",
"id": "#main/save-dir-to-subdir-7/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-7/out"
],
"id": "#main/save-dir-to-subdir-7"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-17/out",
"id": "#main/save-dir-to-subdir-8/inner_dir"
},
{
"source": "#main/mkdir-3/out",
"id": "#main/save-dir-to-subdir-8/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-8/out"
],
"id": "#main/save-dir-to-subdir-8"
},
{
"run": "#save-dir-to-subdir.cwl",
"in": [
{
"source": "#main/save-files-to-dir-18/out",
"id": "#main/save-dir-to-subdir-9/inner_dir"
},
{
"source": "#main/mkdir-3/out",
"id": "#main/save-dir-to-subdir-9/outer_dir"
}
],
"out": [
"#main/save-dir-to-subdir-9/out"
],
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}