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updating filepattern and vaex package
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| ------------------------------------------------ | ||
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| Files : | ||
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| x00_y01_p03_c1.ome.tif -----> x00_y01_p01_c1.ome.tif | ||
| x00_y01_p03_c2.ome.tif -----> x00_y01_p01_c2.ome.tif | ||
| x00_y01_p03_c3.ome.tif -----> x00_y01_p01_c3.ome.tif | ||
| x00_y01_p03_c4.ome.tif -----> x00_y01_p01_c4.ome.tif | ||
| x00_y01_p03_c5.ome.tif -----> x00_y01_p01_c5.ome.tif | ||
| x00_y01_p04_c1.ome.tif -----> x00_y01_p02_c1.ome.tif | ||
| x00_y01_p04_c2.ome.tif -----> x00_y01_p02_c2.ome.tif | ||
| x00_y01_p04_c3.ome.tif -----> x00_y01_p02_c3.ome.tif | ||
| x00_y01_p04_c4.ome.tif -----> x00_y01_p02_c4.ome.tif | ||
| x00_y01_p04_c5.ome.tif -----> x00_y01_p02_c5.ome.tif |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,10 +2,10 @@ | |
| "name": "Feature Subsetting", | ||
| "version": "0.2.0-dev", | ||
| "title": "Feature Subsetting", | ||
| "description": "Subset data using a given feature", | ||
| "description": "Subset data using a given feature.", | ||
| "author": "Gauhar Bains ([email protected]) and Hamdah Shafqat Abbasi ([email protected])", | ||
| "institution": "National Center for Advancing Translational Sciences, National Institutes of Health", | ||
| "repository": "https://github.com/PolusAI/polus-plugin", | ||
| "repository": "https://github.com/PolusAI/polus-plugins", | ||
| "website": "https://ncats.nih.gov/preclinical/core/informatics", | ||
| "citation": "", | ||
| "containerId": "polusai/feature-subsetting-plugin:0.2.0-dev", | ||
|
|
@@ -14,131 +14,160 @@ | |
| "-m", | ||
| "polus.plugins.clustering.feature_subsetting" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "name": "inpDir", | ||
| "inputs": { | ||
| "inpDir": { | ||
| "type": "collection", | ||
| "description": "Input image collection to be processed by this plugin", | ||
| "required": true | ||
| "title": "Input image directory", | ||
| "description": "Input image directory.", | ||
| "required": "True" | ||
| }, | ||
| { | ||
| "name": "filePattern", | ||
| "tabularDir": { | ||
| "type": "genericData", | ||
| "title": "Input tabular directory", | ||
| "description": "Path to directory containing tabular data.", | ||
| "required": "True" | ||
| }, | ||
| "filePattern": { | ||
| "type": "string", | ||
| "title": "Filename pattern", | ||
| "description": "Filename pattern used to separate data.", | ||
| "required": "True" | ||
| }, | ||
| "imageFeature": { | ||
| "type": "string", | ||
| "description": "Filename pattern used to separate data", | ||
| "required": true | ||
| "title": "imageFeature", | ||
| "description": "Feature in tabular data containing image filenames.", | ||
| "required": "True" | ||
| }, | ||
| { | ||
| "name": "groupVar", | ||
| "tabularFeature": { | ||
| "type": "string", | ||
| "description": "variables to group by in a section", | ||
| "required": true | ||
| "title": "tabularFeature", | ||
| "description": "Feature in tabular data to subset image data.", | ||
| "required": "True" | ||
| }, | ||
| { | ||
| "name": "sectionVar", | ||
| "padding": { | ||
| "type": "integer", | ||
| "title": "padding", | ||
| "description": "Number of images to capture outside the cutoff.", | ||
| "required": "False" | ||
| }, | ||
| "groupVar": { | ||
| "type": "string", | ||
| "description": "variables to divide larger sections", | ||
| "required": false | ||
| "title": "groupVar", | ||
| "description": "variables to group by in a section.", | ||
| "required": "True" | ||
| }, | ||
| { | ||
| "name": "csvDir", | ||
| "type": "csvCollection", | ||
| "description": "CSV collection containing features", | ||
| "required": true | ||
| "percentile": { | ||
| "type": "float", | ||
| "title": "percentile", | ||
| "description": "Percentile to remove.", | ||
| "required": "True" | ||
| }, | ||
| { | ||
| "name": "feature", | ||
| "removeDirection": { | ||
| "type": "string", | ||
| "description": "Feature to use to subset data", | ||
| "required": true | ||
| }, | ||
| { | ||
| "name": "percentile", | ||
| "type": "number", | ||
| "description": "Percentile to remove", | ||
| "required": true | ||
| }, | ||
| { | ||
| "name": "removeDirection", | ||
| "type": "enum", | ||
| "options": { | ||
| "values": [ | ||
| "Below", | ||
| "Above" | ||
| ] | ||
| }, | ||
| "description": "remove direction above or below percentile", | ||
| "required": true | ||
| }, | ||
| { | ||
| "name": "padding", | ||
| "title": "removeDirection", | ||
| "description": "Remove direction above or below percentile.", | ||
| "required": "False", | ||
| "default": "Below" | ||
| }, | ||
| "sectionVar": { | ||
| "type": "string", | ||
| "description": "Number of images to capture outside the cutoff", | ||
| "required": false | ||
| "title": "sectionVar", | ||
| "description": "Variables to divide larger sections.", | ||
| "required": "False" | ||
| }, | ||
| "writeOutput": { | ||
| "type": "boolean", | ||
| "title": "writeOutput", | ||
| "description": "Write output image collection or not.", | ||
| "required": "False" | ||
| }, | ||
| { | ||
| "name": "writeOutput", | ||
| "preview": { | ||
| "type": "boolean", | ||
| "description": "write output image collection or not", | ||
| "required": false | ||
| "title": "Preview", | ||
| "description": "Generate an output preview.", | ||
| "required": "False" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "name": "outDir", | ||
| "type": "collection", | ||
| "description": "Output collection" | ||
| }, | ||
| "outputs": { | ||
| "outDir": { | ||
| "type": "genericData", | ||
| "description": "Output collection." | ||
| } | ||
| ], | ||
| "ui": [ | ||
| { | ||
| "key": "inputs.inpDir", | ||
| "title": "Input collection", | ||
| "description": "Input image collection to be processed by this plugin" | ||
| }, | ||
| { | ||
| "key": "inputs.csvDir", | ||
| "title": "CSV collection", | ||
| "description": "CSV collection containing features" | ||
| }, | ||
| { | ||
| "key": "inputs.feature", | ||
| "title": "Feature", | ||
| "description": "Feature to use to subset data" | ||
| }, | ||
| { | ||
| "key": "inputs.percentile", | ||
| "title": "Percentile", | ||
| "description": "Percentile to remove" | ||
| }, | ||
| { | ||
| "key": "inputs.removeDirection", | ||
| "title": "Remove Direction", | ||
| "description": "remove direction above or below percentile" | ||
| }, | ||
| { | ||
| "key": "inputs.filePattern", | ||
| }, | ||
| "ui": { | ||
| "inpDir": { | ||
| "type": "collection", | ||
| "title": "Input image directory", | ||
| "description": "Input image directory.", | ||
| "required": "True" | ||
| }, | ||
| "tabularDir": { | ||
| "type": "genericData", | ||
| "title": "Input tabular directory", | ||
| "description": "Path to directory containing tabular data.", | ||
| "required": "True" | ||
| }, | ||
| "filePattern": { | ||
| "type": "string", | ||
| "title": "Filename pattern", | ||
| "description": "Filename pattern used to separate data" | ||
| }, | ||
| { | ||
| "key": "inputs.groupVar", | ||
| "title": "Grouping Variables", | ||
| "description": "variables to group by in a section" | ||
| }, | ||
| { | ||
| "key": "inputs.sectionVar", | ||
| "title": "Section Variables", | ||
| "description": "variables to divide larger sections" | ||
| }, | ||
| { | ||
| "key": "inputs.padding", | ||
| "title": "Padding", | ||
| "description": "Number of images to capture outside the cutoff" | ||
| }, | ||
| { | ||
| "key": "inputs.writeOutput", | ||
| "title": "Write Output", | ||
| "description": "write output image collection or not" | ||
| "description": "Filename pattern used to separate data.", | ||
| "required": "True" | ||
| }, | ||
| "imageFeature": { | ||
| "type": "string", | ||
| "title": "imageFeature", | ||
| "description": "Feature in tabular data containing image filenames.", | ||
| "required": "True" | ||
| }, | ||
| "tabularFeature": { | ||
| "type": "string", | ||
| "title": "tabularFeature", | ||
| "description": "Feature in tabular data to subset image data.", | ||
| "required": "True" | ||
| }, | ||
| "padding": { | ||
| "type": "integer", | ||
| "title": "padding", | ||
| "description": "Number of images to capture outside the cutoff.", | ||
| "required": "False" | ||
| }, | ||
| "groupVar": { | ||
| "type": "string", | ||
| "title": "groupVar", | ||
| "description": "variables to group by in a section.", | ||
| "required": "True" | ||
| }, | ||
| "percentile": { | ||
| "type": "float", | ||
| "title": "percentile", | ||
| "description": "Percentile to remove.", | ||
| "required": "True" | ||
| }, | ||
| "removeDirection": { | ||
| "type": "string", | ||
| "title": "removeDirection", | ||
| "description": "Remove direction above or below percentile.", | ||
| "required": "False", | ||
| "default": "Below" | ||
| }, | ||
| "sectionVar": { | ||
| "type": "string", | ||
| "title": "sectionVar", | ||
| "description": "Variables to divide larger sections.", | ||
| "required": "False" | ||
| }, | ||
| "writeOutput": { | ||
| "type": "boolean", | ||
| "title": "writeOutput", | ||
| "description": "Write output image collection or not.", | ||
| "required": "False" | ||
| }, | ||
| "preview": { | ||
| "type": "boolean", | ||
| "title": "Preview", | ||
| "description": "Generate an output preview.", | ||
| "required": "False" | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
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