biapy: biapy.xml annotate

author	iuc
date	Thu, 09 Oct 2025 07:42:36 +0000
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0 e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	1 <tool id="biapy" name="Build a workflow with BiaPy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	2 <description>Accessible deep learning on bioimages</description>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	3 <macros>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	4 <import>macros.xml</import>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	5 </macros>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	6 <edam_topics>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	7 <edam_topic>topic_3474</edam_topic> <!-- Machine learning -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	8 <!-- <edam_topic>topic_3753</edam_topic> Deep learning (not in EDAM) -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	9 </edam_topics>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	10 <edam_operations>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	11 <edam_operation>operation_2945</edam_operation> <!-- Image segmentation -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	12 <edam_operation>operation_3925</edam_operation> <!-- Object detection -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	13 <edam_operation>operation_3443</edam_operation> <!-- Image denoising -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	14 <!-- <edam_operation>Single image super-resolution (not in EDAM)</edam_operation> -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	15 <edam_operation>operation_2946</edam_operation> <!-- Image restoration -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	16 <!-- <edam_operation>Image-to-image translation (not in EDAM)</edam_operation> -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	17 <!-- <edam_operation>operation_3442</edam_operation> Image classification -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	18 <!-- <edam_operation>Self-supervision learning (not in EDAM)</edam_operation> -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	19 <edam_operation>operation_2944</edam_operation> <!-- Image analysis -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	20 </edam_operations>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	21 <expand macro="requirements" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	22 <required_files>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	23 <include path="create_yaml.py" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	24 </required_files>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	25 <expand macro="creators" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	26 <command detect_errors="exit_code">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	27 <![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	28 set -xeuo pipefail &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	29 export OPENCV_IO_ENABLE_OPENEXR=0 &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	30
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	31 ## Define some useful variables
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	32 #set $train_raw_dir = './dataset/train/raw'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	33 #set $train_gt_dir = './dataset/train/gt'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	34 #set $test_raw_dir = './dataset/test/raw'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	35 #set $test_gt_dir = './dataset/test/gt'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	36 #set $generated_cfg = 'generated_config.yaml'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	37 #set $checkpoint_dir = './output/my_experiment/checkpoints'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	38 #set $checkpoint_file = $checkpoint_dir + '/checkpoint.safetensors'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	39 #set $common_yaml_args = " --out_config_path '%s' --biapy_version '@TOOL_VERSION@'" % $generated_cfg
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	40
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	41 ## Decide phase and GT availability without touching missing names
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	42 #set $selected_phase = 'train_test'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	43 #set $test_gt_avail = 'test_gt_no'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	44
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	45 #if $mode_selection['selected_mode'] == 'create_new_cfg'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	46 #set $selected_phase = $mode_selection['phase_decision']['phases']
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	47 #if $selected_phase in ['train_test', 'test']
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	48 #set $test_gt_avail = (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	49 $mode_selection['phase_decision'].get('test_sec') and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	50 $mode_selection['phase_decision']['test_sec'].get('gt_test')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	51 ) and 'test_gt_yes' or 'test_gt_no'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	52 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	53 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	54
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	55 ## Define output directory
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	56 mkdir -p output &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	57
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	58 ## Define checkpoint directory in case it is needed
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	59 mkdir -p '$checkpoint_dir' &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	60
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	61 ########## Reuse provided yaml file and update paths ##########
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	62 #if $mode_selection.selected_mode == 'custom_cfg':
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	63 #if $mode_selection.get('test_sec') and $mode_selection['test_sec'].get('gt_test'):
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	64 #set $test_gt_avail = 'test_gt_yes'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	65 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	66 #set $mpath = $mode_selection.get('biapy_model_path')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	67 #if $mpath and str($mpath) not in ['None', '']
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	68 ln -fs '$mpath' ${checkpoint_file} &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	69 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	70 python '$__tool_directory__/create_yaml.py'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	71 --input_config_path '$mode_selection.config_path'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	72 ${common_yaml_args}
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	73 ## Optionally override data paths with the staged dirs if user provided inputs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	74 #if $selected_phase in ['train_test', 'train'] and $mode_selection.get('train_sec') and $mode_selection['train_sec'].get('raw_train')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	75 --raw_train '$train_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	76 #if $mode_selection['train_sec'].get('gt_train')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	77 --gt_train '$train_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	78 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	79 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	80 #if $selected_phase in ['train_test', 'test'] and $mode_selection.get('test_sec') and $mode_selection['test_sec'].get('raw_test')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	81 --test_raw_path '$test_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	82 #if $test_gt_avail == 'test_gt_yes' and $mode_selection['test_sec'].get('gt_test')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	83 --test_gt_path '$test_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	84 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	85 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	86 #if $mpath and str($mpath) not in ['None', '']
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	87 --model '$checkpoint_file'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	88 --model_source 'biapy'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	89 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	90 #else
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	91 ########## Create new yaml file ##########
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	92 #set $pm = $mode_selection["pretrained_model"]
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	93 python '$__tool_directory__/create_yaml.py'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	94 --new_config
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	95 ${common_yaml_args}
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	96 --workflow '$mode_selection["workflow"]'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	97 --dims '$mode_selection["dimensionality"]["is_3d"]'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	98 --obj_slices '$mode_selection["dimensionality"].get("obj_slices")'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	99 --obj_size '$mode_selection["obj_size"]'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	100 --img_channel '$mode_selection["img_channel"]'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	101 #if $pm["model_source"] == 'biapy'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	102 --model_source 'biapy'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	103 #elif $pm["model_source"] == 'biapy_pretrained'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	104 --model '$checkpoint_file'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	105 --model_source 'biapy'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	106 #elif $pm.get("model_source") == 'bmz_torchvision' and $pm.get("bmz_torchvision_model")
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	107 #set $bt = $pm["bmz_torchvision_model"].get("bmz_or_torchvision", "")
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	108 #if $bt == 'bmz'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	109 --model_source 'bmz'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	110 --model '$pm["bmz_torchvision_model"].get("bmz_model_name", "")'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	111 #else
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	112 --model_source 'torchvision'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	113 --model '$pm["bmz_torchvision_model"].get("torchvision_model_name", "")'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	114 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	115 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	116 #if $selected_phase == 'train_test'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	117 --raw_train '$train_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	118 --gt_train '$train_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	119 --test_raw_path '$test_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	120 #if $test_gt_avail == 'test_gt_yes'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	121 --test_gt_path '$test_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	122 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	123 #elif $selected_phase == 'train'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	124 --raw_train '$train_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	125 --gt_train '$train_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	126 #elif $selected_phase == 'test'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	127 --test_raw_path '$test_raw_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	128 #if $test_gt_avail == 'test_gt_yes'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	129 --test_gt_path '$test_gt_dir'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	130 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	131 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	132
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	133 #if $pm["model_source"] == 'biapy_pretrained'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	134 && ln -fs '$pm["biapy_model_path"]' ${checkpoint_file}
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	135 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	136 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	137
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	138 &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	139
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	140 ## Copy the training data
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	141 #if $selected_phase in ['train_test', 'train']:
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	142 mkdir -p '$train_raw_dir' &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	143 #for $i, $image in enumerate($raw_train)
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	144 #set $ext = $image.ext
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	145 ln -s '$image' ${train_raw_dir}/training-${i}.${ext} &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	146 #end for
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	147 mkdir -p '$train_gt_dir' &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	148 #for $i, $image in enumerate($gt_train)
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	149 #set $ext = $image.ext
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	150 ln -s '$image' ${train_gt_dir}/training-gt-${i}.${ext} &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	151 #end for
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	152 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	153
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	154 ## Copy the test data
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	155 #if $selected_phase in ['train_test', 'test']:
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	156 mkdir -p '$test_raw_dir' &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	157 #for $i, $image in enumerate($raw_test)
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	158 #set $ext = $image.ext
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	159 ln -s '$image' ${test_raw_dir}/test-${i}.${ext} &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	160 #end for
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	161 #if $test_gt_avail == 'test_gt_yes':
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	162 mkdir -p '$test_gt_dir' &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	163 #for $i, $image in enumerate($gt_test)
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	164 #set $ext = $image.ext
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	165 ln -s '$image' ${test_gt_dir}/test-gt-${i}.${ext} &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	166 #end for
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	167 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	168 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	169
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	170 ########## Run BiaPy ##########
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	171 biapy
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	172 --config '$generated_cfg'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	173 --result_dir './output'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	174 --name 'my_experiment'
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	175 --run_id 1
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	176 --gpu \${GALAXY_BIAPY_GPU_STRING:-""}
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	177
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	178 #set $outs = $selected_outputs or []
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	179
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	180 ## Copy the selected output to the correct place
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	181 #if $selected_phase in ['train_test', 'test']:
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	182
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	183 #if 'raw' in $outs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	184 ########
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	185 ## RAW #
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	186 ########
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	187 && mkdir -p raw && {
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	188 ## Instance segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	189 if [ -d "output/my_experiment/results/my_experiment_1/per_image_instances" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	190 mv output/my_experiment/results/my_experiment_1/per_image_instances/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	191
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	192 ## Instance segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	193 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_instances" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	194 mv output/my_experiment/results/my_experiment_1/full_image_instances/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	195
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	196 ## Semantic segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	197 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_binarized" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	198 mv output/my_experiment/results/my_experiment_1/per_image_binarized/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	199
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	200 ## Semantic segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	201 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_binarized" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	202 mv output/my_experiment/results/my_experiment_1/full_image_binarized/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	203
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	204 ## I2I
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	205 elif [ -d "output/my_experiment/results/my_experiment_1/full_image" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	206 mv output/my_experiment/results/my_experiment_1/full_image/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	207
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	208 ## Detection
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	209 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_local_max_check" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	210 mv output/my_experiment/results/my_experiment_1/per_image_local_max_check/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	211
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	212 ## Detection, Denoising, I2I, SSL, SR
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	213 elif [ -d "output/my_experiment/results/my_experiment_1/per_image" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	214 mv output/my_experiment/results/my_experiment_1/per_image/* raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	215
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	216 ## Classification
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	217 elif [ -f "output/my_experiment/results/my_experiment_1/predictions.csv" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	218 mv output/my_experiment/results/my_experiment_1/predictions.csv raw/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	219 fi;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	220 }
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	221 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	222
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	223 #if 'post_proc' in $outs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	224 ##############
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	225 ## POST-PROC #
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	226 ##############
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	227 && mkdir -p post_proc && {
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	228 ## Instance segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	229 if [ -d "output/my_experiment/results/my_experiment_1/per_image_post_processing" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	230 mv output/my_experiment/results/my_experiment_1/per_image_post_processing/* post_proc/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	231
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	232 ## Instance segmentation
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	233 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_post_processing" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	234 mv output/my_experiment/results/my_experiment_1/full_image_post_processing/* post_proc/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	235
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	236 ## Detection
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	237 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_local_max_check_post_proc" ]; then
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	238 mv output/my_experiment/results/my_experiment_1/per_image_local_max_check_post_proc/* post_proc/;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	239 fi;
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	240 }
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	241 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	242
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	243 #if 'metrics' in $outs and $test_gt_avail == "test_gt_yes":
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	244 && mkdir -p metrics &&
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	245 mv output/my_experiment/results/my_experiment_1/test_results_metrics.csv metrics/ 2>/dev/null \|\| true
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	246 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	247 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	248 #if $selected_phase in ['train_test', 'train']:
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	249 #if 'tcharts' in $outs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	250 && mkdir -p train_charts
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	251 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	252 #if 'tlogs' in $outs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	253 && mkdir -p train_logs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	254 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	255 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	256 #if 'checkpoint' in $outs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	257 && mkdir -p checkpoints
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	258 #end if
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	259 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	260 </command>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	261
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	262 <inputs>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	263 <conditional name="mode_selection">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	264 <param name="selected_mode" type="select" label="Do you have a configuration file?">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	265 <option value="custom_cfg" selected="true">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	266 Yes, I already have one and I want to run BiaPy directly.
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	267 </option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	268 <option value="create_new_cfg">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	269 No, I want to create one from scratch.
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	270 </option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	271 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	272 <when value="custom_cfg">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	273 <param name="config_path" type="data" format="yaml" optional="false" label="Select a configuration file" help="Input configuration file"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	274 <param name="biapy_model_path" type="data" format="safetensors" optional="true" label="Select the model checkpoint (if needed)" help="Path to a pre-trained model checkpoint (.safetensors) generated by BiaPy. Use this only if 'MODEL.LOAD_CHECKPOINT' is set to 'True' in your configuration."/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	275 <section name="train_sec" title="If train is enabled select the training images">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	276 <!-- Q9 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	277 <expand macro="train_raw_param_opt"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	278 <!-- Q10 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	279 <expand macro="train_gt_param_opt"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	280 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	281 <section name="test_sec" title="If test is enabled select the test images">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	282 <!-- Q11 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	283 <expand macro="test_raw_param_opt"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	284 <!-- Q13 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	285 <expand macro="test_gt_param_optional"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	286 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	287 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	288 <when value="create_new_cfg">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	289 <conditional name="dimensionality">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	290 <!-- Q1 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	291 <param name="is_3d" type="select" label="Are your images in 3D?" help="Select the type of images you will use: 'No' = 2D images (e.g. (512, 1024, 2)); 'Yes' = 3D images (e.g. (400, 400, 50, 1)); 'No, but output as 3D stack' = process 2D images and combine them into a 3D stack after inference, useful if 2D slices form a larger 3D volume.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	292 <option value="2d" selected="true">No</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	293 <option value="3d">Yes</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	294 <option value="2d_stack">No, but I would like to have a 3D stack output</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	295 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	296 <when value="3d">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	297 <!-- Q7 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	298 <param name="obj_slices" type="select" label="How many slices can an object be represented in?" help="This parameter defines the approximate size of the objects of interest along the Z axis. For example, in nucleus segmentation it refers to how many slices a nucleus spans in the stack; knowing this helps set an appropriate value.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	299 <option value="1-5" selected="true">1-5 slices</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	300 <option value="5-10">5-10 slices</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	301 <option value="10-20">10-20 slices</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	302 <option value="20-60">20-60 slices</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	303 <option value="60+">More than 60 slices</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	304 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	305 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	306 <when value="2d"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	307 <when value="2d_stack"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	308 </conditional>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	309 <!-- Q6 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	310 <param name="obj_size" type="select" label="What is the average object width/height in pixels?" help="This parameter defines the approximate size of the objects of interest in your images; for example, in nucleus segmentation it refers to the typical size of nuclei, and only a rough estimation is needed.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	311 <option value="0-25" selected="true">0-25 px</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	312 <option value="25-100">25-100 px</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	313 <option value="100-200">100-200 px</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	314 <option value="200-500">200-500 px</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	315 <option value="500+">More than 500 px</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	316 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	317 <param name="img_channel" type="integer" value="1" min="1" max="10" label="Input the number of channels of the images" help="This parameter specifies the number of channels in your images; for example, use 3 for RGB images or 1 for grayscale, so the model can correctly interpret the input data."/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	318
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	319 <!-- Q2 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	320 <param name="workflow" type="select" label="Do you want to:" help="Select a workflow to run; see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for further explanation.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	321 <option value="semantic" selected="true">Generate masks of different (or just one) objects/regions within the image</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	322 <option value="instance">Generate masks for each object in the image</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	323 <option value="detection">Identify and count roughly circular objects in the images, without needing an exact outline around each one</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	324 <option value="denoising">Clean noisy images</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	325 <option value="sr">Upsample images into higher resolution</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	326 <option value="cls">Assign a label to each image</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	327 <option value="sr2">Restore a degraded image</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	328 <option value="i2i">Generate new images based on an input one</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	329 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	330
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	331 <conditional name="pretrained_model">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	332 <!-- Q3 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	333 <param name="model_source" type="select" label="Do you want to use a pre-trained model?" help="This parameter defines how the deep learning model will be built: (1) build from scratch based on the workflow and image size, (2) load a model previously trained in BiaPy (checkpoint .safetensors in the results/checkpoints folder), or (3) load a pre-trained model from external sources such as the BioImage Model Zoo or Torchvision; training requires labeled data, but pre-trained models can save time and improve results if they match your task.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	334 <option value="biapy" selected="true">No, I want to build a model from scratch</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	335 <option value="biapy_pretrained">Yes, I have a model previously trained in BiaPy</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	336 <option value="bmz_torchvision">Yes, I want to check if there is a pre-trained model I can use</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	337 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	338 <when value="biapy_pretrained">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	339 <!-- Q4 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	340 <param name="biapy_model_path" type="data" format="data" optional="false" label="Select the model trained with BiaPy before" help="Select a pre-trained BiaPy model checkpoint (.safetensors) to use for inference or to resume training. Checkpoints are typically generated by previous BiaPy training runs and appear in your Galaxy history as output datasets."/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	341 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	342 <when value="bmz_torchvision">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	343 <!-- Q5 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	344 <conditional name="bmz_torchvision_model">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	345 <param name="bmz_or_torchvision" type="select" label="Which is the source of the model?" help="Enter the source of the model, whether if it is available through the BioImage Model Zoo or TorchVision">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	346 <option value="bmz" selected="true">BioImage Model Zoo</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	347 <option value="torchvision">TorchVision</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	348 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	349 <when value="bmz">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	350 <param name="bmz_model_name" type="text" optional="false" value="sensible-cat" label="BioImage Model Zoo model name" help="Enter the name of a pre-trained model from the BioImage Model Zoo (https://bioimage.io/#/models); filter by the BiaPy icon and ensure the model matches your dimensionality (2D/3D) and task (e.g. semantic segmentation).">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	351 <validator type="regex" message="Use an adjective-noun pattern like 'sensible-cat' (letters and dashes only).">^[A-Za-z]+(?:-[A-Za-z]+)+$</validator>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	352 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	353 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	354 <when value="torchvision">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	355 <param name="torchvision_model_name" type="text" optional="false" label="TorchVision model name" help="Enter the name of a pre-trained model from TorchVision (see https://docs.pytorch.org/vision/0.21/models.html#general-information-on-pre-trained-weights), e.g. 'alexnet' for classification.">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	356 <validator type="regex" message="Only letters, digits, underscores and dots; must start with a letter.">^[a-zA-Z][a-zA-Z0-9_\.]*$</validator>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	357 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	358 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	359 </conditional>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	360 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	361 <when value="biapy"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	362 </conditional>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	363
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	364 <conditional name="phase_decision">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	365 <!-- Q8 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	366 <param name="phases" type="select" label="What do you want to do?" help="Select which workflow phases to run: training (fit the model to labeled data) and/or testing (inference/prediction on new images using the trained model).">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	367 <option value="train_test" selected="true">Train and test a model</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	368 <option value="train">Train a model</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	369 <option value="test">Test a model</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	370 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	371 <when value="train_test">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	372 <section name="train_sec" title="Train data" expanded="True">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	373 <!-- Q9 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	374 <expand macro="train_raw_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	375 <!-- Q10 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	376 <expand macro="train_gt_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	377 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	378 <section name="test_sec" title="Test data" expanded="True">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	379 <!-- Q11 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	380 <expand macro="test_raw_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	381 <!-- Optional test GT -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	382 <expand macro="test_gt_param_optional"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	383 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	384 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	385
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	386 <when value="train">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	387 <section name="train_sec" title="Train data" expanded="True">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	388 <!-- Q9 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	389 <expand macro="train_raw_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	390 <!-- Q10 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	391 <expand macro="train_gt_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	392 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	393 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	394
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	395 <when value="test">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	396 <section name="test_sec" title="Test data" expanded="True">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	397 <!-- Q11 -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	398 <expand macro="test_raw_param"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	399 <!-- Optional test GT -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	400 <expand macro="test_gt_param_optional"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	401 </section>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	402 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	403 </conditional>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	404 </when>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	405 </conditional>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	406 <param name="selected_outputs" type="select" display="checkboxes" multiple="true" label="Select the outputs" help="Select which outputs to generate from running BiaPy (e.g. predictions, metrics, logs, or intermediate results).">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	407 <option value="raw" selected="true">Test predictions (if exist)</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	408 <option value="post_proc">Post-processed test predictions (if exist)</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	409 <option value="metrics">Evaluation metrics (if exist, on test data)</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	410 <option value="tcharts">Training charts (if exist)</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	411 <option value="tlogs">Training logs (if exist)</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	412 <option value="checkpoint">Model checkpoint</option>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	413 </param>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	414
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	415 </inputs>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	416
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	417 <outputs>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	418 <collection name="predictions_raw" type="list" label="${tool.name} on ${on_string}: Test predictions">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	419 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.tif" format="tif" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	420 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.tiff" format="tiff" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	421 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	422 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.h5" format="h5" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	423 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	424 'raw' in selected_outputs and (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	425 (mode_selection['selected_mode'] == 'create_new_cfg' and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	426 mode_selection['phase_decision']['phases'] in ['test','train_test'])
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	427 or
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	428 (mode_selection['selected_mode'] == 'custom_cfg')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	429 )
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	430 ]]></filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	431 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	432
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	433 <collection name="predictions_post_proc" type="list" label="${tool.name} on ${on_string}: Post-processed test predictions">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	434 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.tif" format="tif" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	435 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.tiff" format="tiff" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	436 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false"/>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	437 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.h5" format="h5" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	438 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	439 'post_proc' in selected_outputs and (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	440 (mode_selection['selected_mode'] == 'create_new_cfg' and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	441 mode_selection['phase_decision']['phases'] in ['test','train_test'])
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	442 or
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	443 (mode_selection['selected_mode'] == 'custom_cfg')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	444 )
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	445 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	446 </filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	447 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	448
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	449 <collection name="test_metrics" type="list" label="${tool.name} on ${on_string}: Test metrics">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	450 <discover_datasets directory="metrics" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	451 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	452 'metrics' in selected_outputs and (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	453 (mode_selection['selected_mode'] == 'create_new_cfg' and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	454 mode_selection['phase_decision']['phases'] in ['test','train_test'] and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	455 mode_selection['phase_decision'].get('test_sec') and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	456 mode_selection['phase_decision']['test_sec'].get('gt_test'))
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	457 or
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	458 (mode_selection['selected_mode'] == 'custom_cfg')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	459 )
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	460 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	461 </filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	462 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	463
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	464 <collection name="train_charts" type="list" label="${tool.name} on ${on_string}: Training charts">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	465 <discover_datasets directory="output/my_experiment/results/my_experiment_1/charts" pattern="(?P<designation>.+)\.png" format="png" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	466 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	467 'tcharts' in selected_outputs and (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	468 (mode_selection['selected_mode'] == 'create_new_cfg' and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	469 mode_selection['phase_decision']['phases'] in ['train','train_test'])
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	470 or
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	471 (mode_selection['selected_mode'] == 'custom_cfg')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	472 )
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	473 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	474 </filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	475 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	476
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	477 <collection name="train_logs" type="list" label="${tool.name} on ${on_string}: Training logs">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	478 <discover_datasets directory="output/my_experiment/train_logs" pattern="(?P<designation>.+)\.txt" format="txt" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	479 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	480 'tlogs' in selected_outputs and (
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	481 (mode_selection['selected_mode'] == 'create_new_cfg' and
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	482 mode_selection['phase_decision']['phases'] in ['train','train_test'])
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	483 or
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	484 (mode_selection['selected_mode'] == 'custom_cfg')
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	485 )
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	486 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	487 </filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	488 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	489
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	490 <collection name="model_checkpoint" type="list" label="${tool.name} on ${on_string}: Model checkpoint">
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	491 <discover_datasets pattern="(?P<designation>.+)\.safetensors" format="data" directory="output/my_experiment/checkpoints" recurse="false" />
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	492 <filter><![CDATA[
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	493 'checkpoint' in selected_outputs
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	494 ]]>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	495 </filter>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	496 </collection>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	497 </outputs>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	498 <tests>
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	499 <!-- test1: test with custom cfg -->
e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0 iuc parents: diff changeset	500 <test expect_num_outputs="2">

0

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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1 <tool id="biapy" name="Build a workflow with BiaPy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">

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2 <description>Accessible deep learning on bioimages</description>

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3 <macros>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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4 <import>macros.xml</import>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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5 </macros>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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6 <edam_topics>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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7 <edam_topic>topic_3474</edam_topic>

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8

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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9 </edam_topics>

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10 <edam_operations>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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11 <edam_operation>operation_2945</edam_operation>

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12 <edam_operation>operation_3925</edam_operation>

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13 <edam_operation>operation_3443</edam_operation>

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14

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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15 <edam_operation>operation_2946</edam_operation>

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16

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17

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18

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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19 <edam_operation>operation_2944</edam_operation>

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20 </edam_operations>

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21 <expand macro="requirements" />

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22 <required_files>

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23 <include path="create_yaml.py" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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24 </required_files>

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25 <expand macro="creators" />

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26 <command detect_errors="exit_code">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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27 <![CDATA[

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28 set -xeuo pipefail &&

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29 export OPENCV_IO_ENABLE_OPENEXR=0 &&

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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30

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31 ## Define some useful variables

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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32 #set $train_raw_dir = './dataset/train/raw'

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33 #set $train_gt_dir = './dataset/train/gt'

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34 #set $test_raw_dir = './dataset/test/raw'

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35 #set $test_gt_dir = './dataset/test/gt'

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36 #set $generated_cfg = 'generated_config.yaml'

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37 #set $checkpoint_dir = './output/my_experiment/checkpoints'

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38 #set $checkpoint_file = $checkpoint_dir + '/checkpoint.safetensors'

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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39 #set $common_yaml_args = " --out_config_path '%s' --biapy_version '@TOOL_VERSION@'" % $generated_cfg

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40

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41 ## Decide phase and GT availability without touching missing names

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42 #set $selected_phase = 'train_test'

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43 #set $test_gt_avail = 'test_gt_no'

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44

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45 #if $mode_selection['selected_mode'] == 'create_new_cfg'

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46 #set $selected_phase = $mode_selection['phase_decision']['phases']

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47 #if $selected_phase in ['train_test', 'test']

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48 #set $test_gt_avail = (

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49 $mode_selection['phase_decision'].get('test_sec') and

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50 $mode_selection['phase_decision']['test_sec'].get('gt_test')

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51 ) and 'test_gt_yes' or 'test_gt_no'

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52 #end if

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53 #end if

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54

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55 ## Define output directory

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56 mkdir -p output &&

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57

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58 ## Define checkpoint directory in case it is needed

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59 mkdir -p '$checkpoint_dir' &&

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60

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61 ########## Reuse provided yaml file and update paths ##########

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62 #if $mode_selection.selected_mode == 'custom_cfg':

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63 #if $mode_selection.get('test_sec') and $mode_selection['test_sec'].get('gt_test'):

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64 #set $test_gt_avail = 'test_gt_yes'

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65 #end if

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66 #set $mpath = $mode_selection.get('biapy_model_path')

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67 #if $mpath and str($mpath) not in ['None', '']

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68 ln -fs '$mpath' ${checkpoint_file} &&

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69 #end if

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70 python '$__tool_directory__/create_yaml.py'

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71 --input_config_path '$mode_selection.config_path'

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72 ${common_yaml_args}

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73 ## Optionally override data paths with the staged dirs if user provided inputs

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74 #if $selected_phase in ['train_test', 'train'] and $mode_selection.get('train_sec') and $mode_selection['train_sec'].get('raw_train')

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75 --raw_train '$train_raw_dir'

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76 #if $mode_selection['train_sec'].get('gt_train')

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77 --gt_train '$train_gt_dir'

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78 #end if

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79 #end if

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80 #if $selected_phase in ['train_test', 'test'] and $mode_selection.get('test_sec') and $mode_selection['test_sec'].get('raw_test')

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81 --test_raw_path '$test_raw_dir'

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82 #if $test_gt_avail == 'test_gt_yes' and $mode_selection['test_sec'].get('gt_test')

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83 --test_gt_path '$test_gt_dir'

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84 #end if

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85 #end if

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86 #if $mpath and str($mpath) not in ['None', '']

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87 --model '$checkpoint_file'

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88 --model_source 'biapy'

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89 #end if

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90 #else

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91 ########## Create new yaml file ##########

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92 #set $pm = $mode_selection["pretrained_model"]

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93 python '$__tool_directory__/create_yaml.py'

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94 --new_config

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95 ${common_yaml_args}

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96 --workflow '$mode_selection["workflow"]'

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97 --dims '$mode_selection["dimensionality"]["is_3d"]'

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98 --obj_slices '$mode_selection["dimensionality"].get("obj_slices")'

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99 --obj_size '$mode_selection["obj_size"]'

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100 --img_channel '$mode_selection["img_channel"]'

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101 #if $pm["model_source"] == 'biapy'

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102 --model_source 'biapy'

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103 #elif $pm["model_source"] == 'biapy_pretrained'

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104 --model '$checkpoint_file'

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105 --model_source 'biapy'

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106 #elif $pm.get("model_source") == 'bmz_torchvision' and $pm.get("bmz_torchvision_model")

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107 #set $bt = $pm["bmz_torchvision_model"].get("bmz_or_torchvision", "")

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108 #if $bt == 'bmz'

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109 --model_source 'bmz'

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110 --model '$pm["bmz_torchvision_model"].get("bmz_model_name", "")'

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111 #else

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112 --model_source 'torchvision'

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113 --model '$pm["bmz_torchvision_model"].get("torchvision_model_name", "")'

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114 #end if

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115 #end if

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116 #if $selected_phase == 'train_test'

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117 --raw_train '$train_raw_dir'

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118 --gt_train '$train_gt_dir'

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119 --test_raw_path '$test_raw_dir'

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120 #if $test_gt_avail == 'test_gt_yes'

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121 --test_gt_path '$test_gt_dir'

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122 #end if

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123 #elif $selected_phase == 'train'

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124 --raw_train '$train_raw_dir'

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125 --gt_train '$train_gt_dir'

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126 #elif $selected_phase == 'test'

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127 --test_raw_path '$test_raw_dir'

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128 #if $test_gt_avail == 'test_gt_yes'

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129 --test_gt_path '$test_gt_dir'

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130 #end if

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131 #end if

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132

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133 #if $pm["model_source"] == 'biapy_pretrained'

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134 && ln -fs '$pm["biapy_model_path"]' ${checkpoint_file}

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135 #end if

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136 #end if

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137

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138 &&

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139

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140 ## Copy the training data

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141 #if $selected_phase in ['train_test', 'train']:

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142 mkdir -p '$train_raw_dir' &&

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143 #for $i, $image in enumerate($raw_train)

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144 #set $ext = $image.ext

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145 ln -s '$image' ${train_raw_dir}/training-${i}.${ext} &&

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146 #end for

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147 mkdir -p '$train_gt_dir' &&

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148 #for $i, $image in enumerate($gt_train)

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149 #set $ext = $image.ext

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150 ln -s '$image' ${train_gt_dir}/training-gt-${i}.${ext} &&

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151 #end for

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152 #end if

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153

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154 ## Copy the test data

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155 #if $selected_phase in ['train_test', 'test']:

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156 mkdir -p '$test_raw_dir' &&

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157 #for $i, $image in enumerate($raw_test)

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158 #set $ext = $image.ext

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159 ln -s '$image' ${test_raw_dir}/test-${i}.${ext} &&

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160 #end for

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161 #if $test_gt_avail == 'test_gt_yes':

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162 mkdir -p '$test_gt_dir' &&

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163 #for $i, $image in enumerate($gt_test)

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164 #set $ext = $image.ext

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165 ln -s '$image' ${test_gt_dir}/test-gt-${i}.${ext} &&

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166 #end for

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167 #end if

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168 #end if

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169

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170 ########## Run BiaPy ##########

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171 biapy

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172 --config '$generated_cfg'

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173 --result_dir './output'

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174 --name 'my_experiment'

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175 --run_id 1

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176 --gpu \${GALAXY_BIAPY_GPU_STRING:-""}

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177

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178 #set $outs = $selected_outputs or []

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179

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180 ## Copy the selected output to the correct place

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181 #if $selected_phase in ['train_test', 'test']:

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182

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183 #if 'raw' in $outs

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184 ########

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185 ## RAW #

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186 ########

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187 && mkdir -p raw && {

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188 ## Instance segmentation

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189 if [ -d "output/my_experiment/results/my_experiment_1/per_image_instances" ]; then

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190 mv output/my_experiment/results/my_experiment_1/per_image_instances/* raw/;

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191

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192 ## Instance segmentation

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193 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_instances" ]; then

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194 mv output/my_experiment/results/my_experiment_1/full_image_instances/* raw/;

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195

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196 ## Semantic segmentation

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197 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_binarized" ]; then

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198 mv output/my_experiment/results/my_experiment_1/per_image_binarized/* raw/;

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199

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200 ## Semantic segmentation

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201 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_binarized" ]; then

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202 mv output/my_experiment/results/my_experiment_1/full_image_binarized/* raw/;

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203

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204 ## I2I

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205 elif [ -d "output/my_experiment/results/my_experiment_1/full_image" ]; then

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206 mv output/my_experiment/results/my_experiment_1/full_image/* raw/;

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207

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208 ## Detection

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209 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_local_max_check" ]; then

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210 mv output/my_experiment/results/my_experiment_1/per_image_local_max_check/* raw/;

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211

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212 ## Detection, Denoising, I2I, SSL, SR

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213 elif [ -d "output/my_experiment/results/my_experiment_1/per_image" ]; then

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214 mv output/my_experiment/results/my_experiment_1/per_image/* raw/;

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215

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216 ## Classification

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217 elif [ -f "output/my_experiment/results/my_experiment_1/predictions.csv" ]; then

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218 mv output/my_experiment/results/my_experiment_1/predictions.csv raw/;

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219 fi;

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220 }

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221 #end if

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222

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223 #if 'post_proc' in $outs

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224 ##############

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225 ## POST-PROC #

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226 ##############

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227 && mkdir -p post_proc && {

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228 ## Instance segmentation

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229 if [ -d "output/my_experiment/results/my_experiment_1/per_image_post_processing" ]; then

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230 mv output/my_experiment/results/my_experiment_1/per_image_post_processing/* post_proc/;

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231

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232 ## Instance segmentation

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233 elif [ -d "output/my_experiment/results/my_experiment_1/full_image_post_processing" ]; then

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234 mv output/my_experiment/results/my_experiment_1/full_image_post_processing/* post_proc/;

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235

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236 ## Detection

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237 elif [ -d "output/my_experiment/results/my_experiment_1/per_image_local_max_check_post_proc" ]; then

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238 mv output/my_experiment/results/my_experiment_1/per_image_local_max_check_post_proc/* post_proc/;

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239 fi;

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240 }

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241 #end if

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242

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243 #if 'metrics' in $outs and $test_gt_avail == "test_gt_yes":

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244 && mkdir -p metrics &&

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245 mv output/my_experiment/results/my_experiment_1/test_results_metrics.csv metrics/ 2>/dev/null || true

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246 #end if

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247 #end if

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248 #if $selected_phase in ['train_test', 'train']:

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249 #if 'tcharts' in $outs

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250 && mkdir -p train_charts

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251 #end if

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252 #if 'tlogs' in $outs

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253 && mkdir -p train_logs

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254 #end if

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255 #end if

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256 #if 'checkpoint' in $outs

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257 && mkdir -p checkpoints

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258 #end if

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259 ]]>

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260 </command>

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261

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262 <inputs>

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263 <conditional name="mode_selection">

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264 <param name="selected_mode" type="select" label="Do you have a configuration file?">

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265 <option value="custom_cfg" selected="true">

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266 Yes, I already have one and I want to run BiaPy directly.

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267 </option>

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268 <option value="create_new_cfg">

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269 No, I want to create one from scratch.

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270 </option>

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271 </param>

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272 <when value="custom_cfg">

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273 <param name="config_path" type="data" format="yaml" optional="false" label="Select a configuration file" help="Input configuration file"/>

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274 <param name="biapy_model_path" type="data" format="safetensors" optional="true" label="Select the model checkpoint (if needed)" help="Path to a pre-trained model checkpoint (.safetensors) generated by BiaPy. Use this only if 'MODEL.LOAD_CHECKPOINT' is set to 'True' in your configuration."/>

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275 <section name="train_sec" title="If train is enabled select the training images">

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276

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277 <expand macro="train_raw_param_opt"/>

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278

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279 <expand macro="train_gt_param_opt"/>

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280 </section>

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281 <section name="test_sec" title="If test is enabled select the test images">

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282

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283 <expand macro="test_raw_param_opt"/>

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284

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285 <expand macro="test_gt_param_optional"/>

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286 </section>

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287 </when>

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288 <when value="create_new_cfg">

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289 <conditional name="dimensionality">

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290

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291 <param name="is_3d" type="select" label="Are your images in 3D?" help="Select the type of images you will use: 'No' = 2D images (e.g. (512, 1024, 2)); 'Yes' = 3D images (e.g. (400, 400, 50, 1)); 'No, but output as 3D stack' = process 2D images and combine them into a 3D stack after inference, useful if 2D slices form a larger 3D volume.">

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292 <option value="2d" selected="true">No</option>

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293 <option value="3d">Yes</option>

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294 <option value="2d_stack">No, but I would like to have a 3D stack output</option>

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295 </param>

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296 <when value="3d">

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297

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298 <param name="obj_slices" type="select" label="How many slices can an object be represented in?" help="This parameter defines the approximate size of the objects of interest along the Z axis. For example, in nucleus segmentation it refers to how many slices a nucleus spans in the stack; knowing this helps set an appropriate value.">

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299 <option value="1-5" selected="true">1-5 slices</option>

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300 <option value="5-10">5-10 slices</option>

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301 <option value="10-20">10-20 slices</option>

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302 <option value="20-60">20-60 slices</option>

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303 <option value="60+">More than 60 slices</option>

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304 </param>

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305 </when>

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306 <when value="2d"/>

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307 <when value="2d_stack"/>

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308 </conditional>

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309

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310 <param name="obj_size" type="select" label="What is the average object width/height in pixels?" help="This parameter defines the approximate size of the objects of interest in your images; for example, in nucleus segmentation it refers to the typical size of nuclei, and only a rough estimation is needed.">

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311 <option value="0-25" selected="true">0-25 px</option>

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312 <option value="25-100">25-100 px</option>

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313 <option value="100-200">100-200 px</option>

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314 <option value="200-500">200-500 px</option>

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315 <option value="500+">More than 500 px</option>

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316 </param>

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317 <param name="img_channel" type="integer" value="1" min="1" max="10" label="Input the number of channels of the images" help="This parameter specifies the number of channels in your images; for example, use 3 for RGB images or 1 for grayscale, so the model can correctly interpret the input data."/>

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318

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319

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320 <param name="workflow" type="select" label="Do you want to:" help="Select a workflow to run; see https://biapy.readthedocs.io/en/latest/get_started/select_workflow.html for further explanation.">

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321 <option value="semantic" selected="true">Generate masks of different (or just one) objects/regions within the image</option>

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322 <option value="instance">Generate masks for each object in the image</option>

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323 <option value="detection">Identify and count roughly circular objects in the images, without needing an exact outline around each one</option>

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324 <option value="denoising">Clean noisy images</option>

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325 <option value="sr">Upsample images into higher resolution</option>

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326 <option value="cls">Assign a label to each image</option>

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327 <option value="sr2">Restore a degraded image</option>

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328 <option value="i2i">Generate new images based on an input one</option>

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329 </param>

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330

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331 <conditional name="pretrained_model">

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332

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333 <param name="model_source" type="select" label="Do you want to use a pre-trained model?" help="This parameter defines how the deep learning model will be built: (1) build from scratch based on the workflow and image size, (2) load a model previously trained in BiaPy (checkpoint .safetensors in the results/checkpoints folder), or (3) load a pre-trained model from external sources such as the BioImage Model Zoo or Torchvision; training requires labeled data, but pre-trained models can save time and improve results if they match your task.">

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334 <option value="biapy" selected="true">No, I want to build a model from scratch</option>

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335 <option value="biapy_pretrained">Yes, I have a model previously trained in BiaPy</option>

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336 <option value="bmz_torchvision">Yes, I want to check if there is a pre-trained model I can use</option>

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337 </param>

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338 <when value="biapy_pretrained">

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339

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340 <param name="biapy_model_path" type="data" format="data" optional="false" label="Select the model trained with BiaPy before" help="Select a pre-trained BiaPy model checkpoint (.safetensors) to use for inference or to resume training. Checkpoints are typically generated by previous BiaPy training runs and appear in your Galaxy history as output datasets."/>

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341 </when>

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342 <when value="bmz_torchvision">

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343

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344 <conditional name="bmz_torchvision_model">

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345 <param name="bmz_or_torchvision" type="select" label="Which is the source of the model?" help="Enter the source of the model, whether if it is available through the BioImage Model Zoo or TorchVision">

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346 <option value="bmz" selected="true">BioImage Model Zoo</option>

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347 <option value="torchvision">TorchVision</option>

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348 </param>

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349 <when value="bmz">

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350 <param name="bmz_model_name" type="text" optional="false" value="sensible-cat" label="BioImage Model Zoo model name" help="Enter the name of a pre-trained model from the BioImage Model Zoo (https://bioimage.io/#/models); filter by the BiaPy icon and ensure the model matches your dimensionality (2D/3D) and task (e.g. semantic segmentation).">

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351 <validator type="regex" message="Use an adjective-noun pattern like 'sensible-cat' (letters and dashes only).">^[A-Za-z]+(?:-[A-Za-z]+)+$</validator>

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352 </param>

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353 </when>

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354 <when value="torchvision">

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355 <param name="torchvision_model_name" type="text" optional="false" label="TorchVision model name" help="Enter the name of a pre-trained model from TorchVision (see https://docs.pytorch.org/vision/0.21/models.html#general-information-on-pre-trained-weights), e.g. 'alexnet' for classification.">

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356 <validator type="regex" message="Only letters, digits, underscores and dots; must start with a letter.">^[a-zA-Z][a-zA-Z0-9_\.]*$</validator>

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357 </param>

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358 </when>

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359 </conditional>

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360 </when>

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361 <when value="biapy"/>

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362 </conditional>

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363

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364 <conditional name="phase_decision">

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365

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366 <param name="phases" type="select" label="What do you want to do?" help="Select which workflow phases to run: training (fit the model to labeled data) and/or testing (inference/prediction on new images using the trained model).">

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367 <option value="train_test" selected="true">Train and test a model</option>

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368 <option value="train">Train a model</option>

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369 <option value="test">Test a model</option>

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370 </param>

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371 <when value="train_test">

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372 <section name="train_sec" title="Train data" expanded="True">

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373

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374 <expand macro="train_raw_param"/>

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375

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376 <expand macro="train_gt_param"/>

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377 </section>

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378 <section name="test_sec" title="Test data" expanded="True">

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379

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380 <expand macro="test_raw_param"/>

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381

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382 <expand macro="test_gt_param_optional"/>

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383 </section>

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384 </when>

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385

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386 <when value="train">

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387 <section name="train_sec" title="Train data" expanded="True">

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388

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389 <expand macro="train_raw_param"/>

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390

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391 <expand macro="train_gt_param"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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392 </section>

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393 </when>

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394

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395 <when value="test">

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396 <section name="test_sec" title="Test data" expanded="True">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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397

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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398 <expand macro="test_raw_param"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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399

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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400 <expand macro="test_gt_param_optional"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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401 </section>

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402 </when>

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403 </conditional>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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404 </when>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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405 </conditional>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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406 <param name="selected_outputs" type="select" display="checkboxes" multiple="true" label="Select the outputs" help="Select which outputs to generate from running BiaPy (e.g. predictions, metrics, logs, or intermediate results).">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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407 <option value="raw" selected="true">Test predictions (if exist)</option>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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408 <option value="post_proc">Post-processed test predictions (if exist)</option>

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409 <option value="metrics">Evaluation metrics (if exist, on test data)</option>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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410 <option value="tcharts">Training charts (if exist)</option>

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411 <option value="tlogs">Training logs (if exist)</option>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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412 <option value="checkpoint">Model checkpoint</option>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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413 </param>

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414

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415 </inputs>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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416

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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417 <outputs>

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418 <collection name="predictions_raw" type="list" label="${tool.name} on ${on_string}: Test predictions">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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419 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.tif" format="tif" recurse="false"/>

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420 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.tiff" format="tiff" recurse="false"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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421 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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422 <discover_datasets directory="raw" pattern="(?P<designation>.+)\.h5" format="h5" recurse="false"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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423 <filter><![CDATA[

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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424 'raw' in selected_outputs and (

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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425 (mode_selection['selected_mode'] == 'create_new_cfg' and

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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426 mode_selection['phase_decision']['phases'] in ['test','train_test'])

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diff changeset

427 or

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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428 (mode_selection['selected_mode'] == 'custom_cfg')

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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429 )

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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430 ]]></filter>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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431 </collection>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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432

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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433 <collection name="predictions_post_proc" type="list" label="${tool.name} on ${on_string}: Post-processed test predictions">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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434 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.tif" format="tif" recurse="false" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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435 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.tiff" format="tiff" recurse="false"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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436 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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437 <discover_datasets directory="post_proc" pattern="(?P<designation>.+)\.h5" format="h5" recurse="false" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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438 <filter><![CDATA[

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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439 'post_proc' in selected_outputs and (

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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440 (mode_selection['selected_mode'] == 'create_new_cfg' and

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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441 mode_selection['phase_decision']['phases'] in ['test','train_test'])

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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442 or

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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443 (mode_selection['selected_mode'] == 'custom_cfg')

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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444 )

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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445 ]]>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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446 </filter>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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447 </collection>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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448

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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449 <collection name="test_metrics" type="list" label="${tool.name} on ${on_string}: Test metrics">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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450 <discover_datasets directory="metrics" pattern="(?P<designation>.+)\.csv" format="csv" recurse="false" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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451 <filter><![CDATA[

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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452 'metrics' in selected_outputs and (

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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453 (mode_selection['selected_mode'] == 'create_new_cfg' and

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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454 mode_selection['phase_decision']['phases'] in ['test','train_test'] and

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455 mode_selection['phase_decision'].get('test_sec') and

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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456 mode_selection['phase_decision']['test_sec'].get('gt_test'))

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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457 or

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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458 (mode_selection['selected_mode'] == 'custom_cfg')

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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459 )

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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460 ]]>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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461 </filter>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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462 </collection>

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463

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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464 <collection name="train_charts" type="list" label="${tool.name} on ${on_string}: Training charts">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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465 <discover_datasets directory="output/my_experiment/results/my_experiment_1/charts" pattern="(?P<designation>.+)\.png" format="png" recurse="false" />

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466 <filter><![CDATA[

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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467 'tcharts' in selected_outputs and (

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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468 (mode_selection['selected_mode'] == 'create_new_cfg' and

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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469 mode_selection['phase_decision']['phases'] in ['train','train_test'])

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470 or

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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471 (mode_selection['selected_mode'] == 'custom_cfg')

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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472 )

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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473 ]]>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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474 </filter>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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475 </collection>

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476

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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477 <collection name="train_logs" type="list" label="${tool.name} on ${on_string}: Training logs">

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478 <discover_datasets directory="output/my_experiment/train_logs" pattern="(?P<designation>.+)\.txt" format="txt" recurse="false" />

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479 <filter><![CDATA[

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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480 'tlogs' in selected_outputs and (

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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481 (mode_selection['selected_mode'] == 'create_new_cfg' and

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482 mode_selection['phase_decision']['phases'] in ['train','train_test'])

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483 or

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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484 (mode_selection['selected_mode'] == 'custom_cfg')

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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485 )

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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486 ]]>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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487 </filter>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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488 </collection>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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489

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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490 <collection name="model_checkpoint" type="list" label="${tool.name} on ${on_string}: Model checkpoint">

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491 <discover_datasets pattern="(?P<designation>.+)\.safetensors" format="data" directory="output/my_experiment/checkpoints" recurse="false" />

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492 <filter><![CDATA[

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493 'checkpoint' in selected_outputs

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494 ]]>

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495 </filter>

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496 </collection>

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497 </outputs>

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498 <tests>

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499

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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500 <test expect_num_outputs="2">

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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501

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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502 <param name="mode_selection|selected_mode" value="custom_cfg"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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503

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504 <param name="mode_selection|config_path" value="example.yaml"/>

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505 <param name="mode_selection|test_sec|raw_test" value="im_0000.png"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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506 <param name="mode_selection|test_sec|gt_test" value="mask_0000.png"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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507 <param name="selected_outputs" value="raw,metrics"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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508 <output_collection name="predictions_raw" type="list" count="1" />

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509 <output_collection name="test_metrics" type="list" count="1"/>

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510 <assert_command>

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511 <has_text text="--config 'generated_config.yaml'"/>

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512 <has_text text="--result_dir './output'"/>

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513 <has_text text="--name 'my_experiment'"/>

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514 <has_text text="--run_id 1"/>

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515 </assert_command>

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516 </test>

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517

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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518

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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519 <test expect_num_outputs="2">

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520

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521 <param name="mode_selection|selected_mode" value="create_new_cfg" />

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522

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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523

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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524 <param name="mode_selection|dimensionality|is_3d" value="2d" />

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525

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526

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527 <param name="mode_selection|obj_size" value="0-25" />

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528 <param name="mode_selection|img_channel" value="1" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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529

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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530

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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531 <param name="mode_selection|workflow" value="semantic" />

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532

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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533

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534 <param name="mode_selection|pretrained_model|model_source" value="bmz_torchvision" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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535 <param name="mode_selection|pretrained_model|bmz_torchvision_model|bmz_or_torchvision" value="bmz" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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536 <param name="mode_selection|pretrained_model|bmz_torchvision_model|bmz_model_name" value="sensible-cat" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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537

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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538

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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539 <param name="mode_selection|phase_decision|phases" value="test" />

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540

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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541

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542 <param name="mode_selection|phase_decision|test_sec|raw_test" value="im_0000.png" />

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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543 <param name="mode_selection|phase_decision|test_sec|gt_test" value="mask_0000.png" />

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544

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545

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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546 <param name="selected_outputs" value="raw,metrics" />

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547 <output_collection name="predictions_raw" type="list" count="1" />

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548 <output_collection name="test_metrics" type="list" count="1"/>

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549 <assert_command>

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550 <has_text text="--config 'generated_config.yaml'"/>

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551 <has_text text="--result_dir './output'"/>

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552 <has_text text="--name 'my_experiment'"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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553 <has_text text="--run_id 1"/>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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554 </assert_command>

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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555 </test>

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diff changeset

556

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557

e434d9b9cd13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy/ commit 66b393a7118c81d86d0fd80780d2bd551c18f3f0

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558 <test expect_num_outputs="1">

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559

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560 <param name="mode_selection|selected_mode" value="create_new_cfg" />

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561

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562

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563 <param name="mode_selection|dimensionality|is_3d" value="2d" />

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564

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565

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566 <param name="mode_selection|obj_size" value="25-100" />

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567 <param name="mode_selection|img_channel" value="1" />

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568

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569

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570 <param name="mode_selection|workflow" value="denoising" />

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571

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573 <param name="mode_selection|pretrained_model|model_source" value="biapy" />

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574

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575

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576 <param name="mode_selection|phase_decision|phases" value="test" />

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577

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578

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579 <param name="mode_selection|phase_decision|test_sec|raw_test" value="im_0000.png" />

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580

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581

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582 <param name="selected_outputs" value="raw" />

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583 <output_collection name="predictions_raw" type="list" count="1" />

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584 <assert_command>

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585 <has_text text="--config 'generated_config.yaml'"/>

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586 <has_text text="--result_dir './output'"/>

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587 <has_text text="--name 'my_experiment'"/>

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588 <has_text text="--run_id 1"/>

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589 </assert_command>

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590 </test>

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591

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592 </tests>

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593 <help><![CDATA[

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594 **What it does**

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595

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596 This tool runs a BiaPy workflow for image analysis using deep learning models. BiaPy is a bioimage analysis pipeline designed to simplify training, prediction, and evaluation across a variety of tasks such as image segmentation, classification, denoising, and more.

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597

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598 ---

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599

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600 **Usage**

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601

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602 There are two main usage modes for this tool:

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603

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604 1. **Using a custom configuration file (YAML)**

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605 If you already have a BiaPy configuration file, you can upload it directly. The tool will use this configuration without further modification to run the specified BiaPy workflow.

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606

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607 2. **Constructing a configuration interactively**

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608 If you do not have a YAML configuration file, the tool can help you build one by asking a set of guided questions. This includes settings like:

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609 - Task type (e.g., segmentation, classification)

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610 - Model architecture

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611 - Input/output patch sizes

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612 - Data paths and formats

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613 - Training parameters (epochs, batch size, etc.)

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614

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615 Once these options are specified, the tool generates a valid BiaPy YAML config and proceeds to execute the workflow.

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616

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617 ---

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618

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619 **Output**

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620

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621 The output depends on the chosen workflow and may include:

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622 - Trained model weights

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623 - Prediction results

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624 - Evaluation metrics (if ground truth is available)

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625 - Log files and training history

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626

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627 ---

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628

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629 **Tips**

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630

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631 - For best results, ensure that your input data format matches what BiaPy expects. Refer to the [BiaPy documentation](https://biapy.readthedocs.io/en/latest/) for details.

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632 - Use the "interactive mode" if you're new to BiaPy and want guidance on configuration.

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633 - Advanced users with pre-tuned configs may prefer uploading a YAML directly for faster execution.

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634

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635 ---

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636

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637 **References**

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638 - BiaPy landing page: https://biapyx.github.io/

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639 - BiaPy documentation: https://biapy.readthedocs.io/

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640 - Galaxy Tool Development: https://galaxyproject.org/tools/

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641 ]]></help>

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642 <expand macro="citations"/>

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643 </tool>

Mercurial > repos > iuc > biapy

annotate biapy.xml @ 0:e434d9b9cd13 draft default tip