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cnn-training.cwl.yml
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cnn-training.cwl.yml
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cwlVersion: v1.0
class: CommandLineTool
baseCommand:
- camelyon-cnns
doc: "CAMELYON CNNs trains Convolutional Neural Networks on the CAMELYON image database."
inputs:
hdf5:
type: Directory
inputBinding:
position: 0
doc: "File path to hdf5 file. Can also be a directory path, if the directory contains a file called merged.hdf5."
arch:
type: string?
inputBinding:
prefix: --arch
doc: "Architecture to use. 0=VGG16 (not working yet), 1=InceptionV3, 2=InceptionResNetV2."
batch_size_neg:
type: string?
inputBinding:
prefix: --batch-size-neg
doc: "Batch size for negative examples."
batch_size_pos:
type: string?
inputBinding:
prefix: --batch-size-pos
doc: 'Batch size for positive examples.'
batches_train:
type: string?
inputBinding:
prefix: --batches-train
doc: "Batches per train epoch."
batches_val:
type: string?
inputBinding:
prefix: --batches-val
doc: "Batches per validation epoch."
epochs:
type: string?
inputBinding:
prefix: --epochs
doc: "Epochs to train."
queue_size:
type: string?
inputBinding:
prefix: --queue-size
doc: "Number of batches to preload while training."
l_rate:
type: string?
inputBinding:
prefix: --l-rate
doc: "Number of batches to preload while training."
mask_threshold:
type: string?
inputBinding:
prefix: --mask-threshold
doc: "Threshold of tissue in a cropped 224x224 tile to be valid. Or threshold of tumor tissue in a 224x224 slide to be valid."
color_norm:
type: string?
inputBinding:
prefix: --color-norm
doc: "Colornormalization yes/no (1/0)."
workers:
type: string?
inputBinding:
prefix: --workers
doc: "Number of parallel batch--generator workers. Setting this option enables multiprocessing."
fast_hdf5:
type: string?
inputBinding:
prefix: --fast-hdf5
doc: "Switch HDF5 Format to IO optimized version yes/no (1/0)."
outputs:
log:
type: File
outputBinding:
glob: log.json
doc: "Log file containing performance measurements."
acc_plot:
type: File
outputBinding:
glob: acc.png
doc: "Validation and training accuracy per epoch."
loss_plot:
type: File
outputBinding:
glob: loss.png
doc: "Validation and training loss per epoch."
roc_plot:
type: File
outputBinding:
glob: roc.png
doc: "ROC."
model_final:
type: File
outputBinding:
glob: model_final.hdf5
doc: "Final Model."
checkpoint:
type: File
outputBinding:
glob: checkpoint
model_checkpoint_data:
type: File
outputBinding:
glob: model_checkpoint.ckpt.data*
model_checkpoint_index:
type: File
outputBinding:
glob: model_checkpoint.ckpt.index