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annotate vpt_segment.xml @ 3:0811613196a2 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
author bgruening
date Mon, 11 Aug 2025 08:53:09 +0000
parents a88a1e78702e
children
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1 <tool id="vpt_segment" name="Vizgen VPT - Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>cells and refine MERSCOPE experiments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="creator" />
3
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8 <required_files>
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9 <include path="safetensors_convert_pytorch.py"/>
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10 </required_files>
0
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11 <command detect_errors="exit_code"><![CDATA[
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12 @CMD@
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13 ln -s '$detected_transcripts' 'input/detected_transcripts.csv' &&
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14 ln -s '$vpt_config_file' 'input/vpt_config_file.json' &&
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15 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
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16 #if $task.segmentation_properties.custom_weights:
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17 ln -s '$task.segmentation_properties.custom_weights' 'input/model/custom_weights_${i}.safetensors' &&
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18 python '$__tool_directory__/safetensors_convert_pytorch.py' --convert safe_pt -i 'input/model/custom_weights_${i}.safetensors' -o 'input/model/custom_weights_${i}.pth' &&
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19 #end if
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20 #end for
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21 ### segmentation
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22 vpt
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23 @COMMON_ARGS@
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24 run-segmentation
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25 --segmentation-algorithm 'input/vpt_config_file.json'
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26 --input-images 'input/images/'
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27 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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28 --output-path 'output/'
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29 --tile-size $tile_size
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30 #if $max_row_group_size:
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31 --max-row-group-size $max_row_group_size
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32 #end if
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33 --tile-overlap $tile_overlap &&
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34 ### counting partition transcripts
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35 vpt
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36 @COMMON_ARGS@
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37 partition-transcripts
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38 --input-boundaries 'output/cellpose2_micron_space.parquet'
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39 --input-transcripts 'input/detected_transcripts.csv'
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40 --output-entity-by-gene 'output/cell_by_gene.csv'
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41 --output-transcripts 'output/detected_transcripts.csv' &&
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42 ### sum signals
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43 vpt
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44 @COMMON_ARGS@
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45 sum-signals
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46 --input-images 'input/images/'
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47 --input-boundaries 'output/cellpose2_micron_space.parquet'
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48 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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49 --output-csv 'output/sum_signals.csv' &&
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50 ### derive entity metadata
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51 vpt
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52 @COMMON_ARGS@
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53 derive-entity-metadata
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54 --input-boundaries 'output/cellpose2_micron_space.parquet'
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55 --input-entity-by-gene 'output/cell_by_gene.csv'
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56 --output-metadata 'output/cell_metadata.csv' &&
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57 ### segmentation QC
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58 vpt
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59 @COMMON_ARGS@
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60 generate-segmentation-metrics
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61 --input-entity-by-gene 'output/cell_by_gene.csv'
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62 --input-metadata 'output/cell_metadata.csv'
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63 --input-transcripts 'output/detected_transcripts.csv'
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64 --input-boundaries 'output/cellpose2_micron_space.parquet'
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65 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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66 --input-images 'input/images/'
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67 --experiment-name '$qc_params.experiment_name'
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68 --input-z-index '$qc_params.input_z_index'
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69 #if $qc_params.red_stain_name != "None":
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70 --red-stain-name '$qc_params.red_stain_name'
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71 #end if
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72 #if $qc_params.green_stain_name != "None":
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73 --green-stain-name '$qc_params.green_stain_name'
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74 #end if
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75 #if $qc_params.blue_stain_name != "None":
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76 --blue-stain-name '$qc_params.blue_stain_name'
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77 #end if
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78 --transcript-count-filter-threshold '$qc_params.transcript_count_filter_threshold'
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79 --volume-filter-threshold '$qc_params.volume_filter_threshold'
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80 --output-csv 'output/metrics.csv'
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81 --output-report 'output/metrics.html'
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82 --output-clustering 'output/metrics_clustering.parquet' &&
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83 mv 'input/vpt_config_file.json' 'output/vpt_config_file.json'
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84 ]]></command>
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85 <configfiles>
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86 <configfile name="vpt_config_file"><![CDATA[
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87 {
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88 "experiment_properties": {
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89 #set $indices = ",".join([str(i) for i in range(len(str($vpt_config.experiment_properties.z_positions_um.value).split(",")))])
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90
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91 "all_z_indexes": [$indices],
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92 "z_positions_um": [$vpt_config.experiment_properties.z_positions_um]
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93 },
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94 "segmentation_tasks": [
1
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95 #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
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96 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
0
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97 {
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98 "task_id": $i,
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99 "segmentation_family": "Cellpose2",
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100 #if $task.entity_types_detected != "both":
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101 "entity_types_detected": ["$task.entity_types_detected"],
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102 #else:
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103 "entity_types_detected": [
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104 "nuclei",
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105 "cell"
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106 ],
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107 #end if
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108 "z_layers": [$task.z_layers],
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109 "segmentation_properties": {
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110 #if $task.segmentation_properties.model != "null":
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111 "model": "$task.segmentation_properties.model",
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112 #else:
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113 "model": null,
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114 #end if
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115 "model_dimensions": "$task.segmentation_properties.model_dimensions",
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116 #if $task.segmentation_properties.custom_weights:
3
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117 "custom_weights": "input/model/custom_weights_${i}.pth",
0
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118 #else:
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119 "custom_weights": null,
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120 #end if
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121 "channel_map": {
2
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122 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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123 "red": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
0
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124 #else:
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125 "red": "",
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126 #end if
2
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127 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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128 "green": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
0
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129 #else:
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130 "green": "",
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131 #end if
2
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132 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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133 "blue": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue"
0
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134 #else:
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135 "blue": ""
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136 #end if
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137 }
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138 },
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139 "task_input_data": [
2
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140 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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141 #set $input_data = $task.segmentation_properties.channel_map.channel_red_conditional
0
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142 {
2
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143 "image_channel": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
0
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144 "image_preprocessing": [
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145 #if $input_data.normalize_conditional.normalize_select == "Yes":
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146 {
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147 "name": "normalize",
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148 "parameters": {
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149 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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150 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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151 "filter_size": [
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152 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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153 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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154 ],
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155 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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156 #end if
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157 }
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158 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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159 ,
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160 #end if
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161 #end if
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162 #if $input_data.blur_conditional.blur_select == "Yes":
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163 {
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164 "name": "blur",
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165 "parameters": {
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166 "type": "$input_data.blur_conditional.blur_options",
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167 "size": $input_data.blur_conditional.kernel_size
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168 }
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169 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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170 ,
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171 #end if
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172 #end if
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173 #if $input_data.downsample_conditional.downsample_select == "Yes":
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174 {
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175 "name": "downsample",
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176 "parameters": {
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177 "scale": "$input_data.downsample_conditional.scale"
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178 }
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179 }
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180 #end if
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181 ]
2
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182 }#if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None" or $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
0
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183 ,
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184 #end if
2
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185 #end if
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186 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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187 #set $input_data = $task.segmentation_properties.channel_map.channel_green_conditional
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188 {
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189 "image_channel": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
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190 "image_preprocessing": [
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191 #if $input_data.normalize_conditional.normalize_select == "Yes":
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192 {
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193 "name": "normalize",
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194 "parameters": {
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195 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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196 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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197 "filter_size": [
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198 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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199 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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200 ],
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201 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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202 #end if
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203 }
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204 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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205 ,
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206 #end if
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207 #end if
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208 #if $input_data.blur_conditional.blur_select == "Yes":
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209 {
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210 "name": "blur",
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211 "parameters": {
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212 "type": "$input_data.blur_conditional.blur_options",
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213 "size": $input_data.blur_conditional.kernel_size
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214 }
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215 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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216 ,
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217 #end if
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218 #end if
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219 #if $input_data.downsample_conditional.downsample_select == "Yes":
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220 {
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221 "name": "downsample",
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222 "parameters": {
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223 "scale": "$input_data.downsample_conditional.scale"
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224 }
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225 }
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226 #end if
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227 ]
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228 }#if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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229 ,
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230 #end if
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231 #end if
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232 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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233 #set $input_data = $task.segmentation_properties.channel_map.channel_blue_conditional
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234 {
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235 "image_channel": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue",
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236 "image_preprocessing": [
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237 #if $input_data.normalize_conditional.normalize_select == "Yes":
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238 {
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239 "name": "normalize",
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240 "parameters": {
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241 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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242 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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243 "filter_size": [
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244 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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245 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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246 ],
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247 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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248 #end if
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249 }
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250 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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251 ,
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252 #end if
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253 #end if
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254 #if $input_data.blur_conditional.blur_select == "Yes":
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255 {
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256 "name": "blur",
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257 "parameters": {
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258 "type": "$input_data.blur_conditional.blur_options",
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259 "size": $input_data.blur_conditional.kernel_size
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260 }
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261 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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262 ,
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263 #end if
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264 #end if
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265 #if $input_data.downsample_conditional.downsample_select == "Yes":
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266 {
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267 "name": "downsample",
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268 "parameters": {
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269 "scale": "$input_data.downsample_conditional.scale"
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270 }
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271 }
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272 #end if
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273 ]
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274 }
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275 #end if
0
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276 ],
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277 "segmentation_parameters": {
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278 #if $task.segmentation_parameters.nuclear_channel != "None":
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279 "nuclear_channel": "$task.segmentation_parameters.nuclear_channel",
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280 #else:
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281 "nuclear_channel": null,
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282 #end if
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283 #if $task.segmentation_parameters.entity_fill_channel != "None":
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284 "entity_fill_channel": "$task.segmentation_parameters.entity_fill_channel",
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285 #else:
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286 "entity_fill_channel": null,
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287 #end if
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288 "diameter": $task.segmentation_parameters.diameter,
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289 "flow_threshold": $task.segmentation_parameters.flow_threshold,
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290 "cellprob_threshold": $task.segmentation_parameters.cellprob_threshold,
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291 "minimum_mask_size": $task.segmentation_parameters.minimum_mask_size
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292 },
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293 "polygon_parameters": {
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294 "simplification_tol": $task.polygon_parameters.simplification_tol,
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295 "smoothing_radius": $task.polygon_parameters.smoothing_radius,
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296 "minimum_final_area": $task.polygon_parameters.minimum_final_area
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297 }
1
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298 }#if $i != $task_n
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299 ,
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300 #end if
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301 #end for
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302 ],
0
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303 "segmentation_task_fusion": {
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304 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
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305 "fused_polygon_postprocessing_parameters": {
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306 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities,
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307 "min_final_area": $segmentation_task_fusion.min_final_area
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308 }
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309 },
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310 "output_files": [
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311 {
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312 #if $vpt_config.output_files.entity_types_output != "both":
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313 "entity_types_output": ["$vpt_config.output_files.entity_types_output"],
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314 #else:
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315 "entity_types_output": [
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316 "nuclei",
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317 "cell"
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318 ],
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319 #end if
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320 "files": {
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321 "run_on_tile_dir": "result_tiles/",
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322 "mosaic_geometry_file": "cellpose2_mosaic_space.parquet",
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323 "micron_geometry_file": "cellpose2_micron_space.parquet",
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324 "cell_metadata_file": "cellpose2_cell_metadata.csv"
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325 }
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326 }
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327 ]
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328 }
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329 ]]></configfile>
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330 </configfiles>
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331 <inputs>
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332 <expand macro="common_input"/>
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333 <param argument="--detected_transcripts" type="data" format="csv" label="Detected transcripts"/>
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334 <param argument="--tile_size" type="integer" min="1" value="4096" label="Number of pixels for the width and height of each tile"/>
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335 <param argument="--tile_overlap" type="integer" min="0" max="100" value="10" label="Overlap between adjacent tiles (%)" help="Default: 10% of tile size"/>
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336 <param argument="--max_row_group_size" type="integer" min="1000" value="" optional="true" label="Maximum number of rows in row groups inside output parquet files"/>
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337 <section name="vpt_config" title="Segmentation configuration file">
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338 <section name="experiment_properties" title="Experiment properties" help="Specify the z-indexes and z-positions in the data. It is used to apply 2D segmentation to 3D data and calculate distances on the z-axis.">
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339 <param argument="--z_positions_um" type="text" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5" label="Z-layer positions in micron">
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340 <expand macro="sanitize_digits"/>
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341 </param>
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342 </section>
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343 <section name="segmentation_tasks" title="Segmentation tasks" help="A list of segmentation tasks to perform sequentially. The VPT only supports 9 tasks in a single segmentation algorithm. If more tasks are needed, users are encouraged to run vpt multiple times and combine the segmentation outputs post hoc.">
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344 <repeat name="segmentation_task" min="1" max="9" title="Segmentation tasks">
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345 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?">
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346 <option value="cell">cell</option>
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347 <option value="nucleus">nucleus</option>
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348 <option value="both">both</option>
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349 </param>
1
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350 <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
0
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351 <expand macro="sanitize_digits"/>
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352 </param>
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353 <section name="segmentation_properties" title="Segmentation properties">
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354 <param argument="--model" type="select" label="Cellpose model">
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355 <option value="cyto2">cyto2</option>
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356 <option value="nuclei">nuclei</option>
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357 <option value="null">null</option>
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358 </param>
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359 <param argument="--model_dimensions" type="select" label="Model dimensions" help="2D applies the 2D Cellpose model to all z-planes specified in the z_layers list separately and the results are combined into a 3D output. 3D applies the native-3D Cellpose model to all z-planes specified in the z_layers list.">
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360 <option value="2D">2D</option>
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361 <option value="3D">3D</option>
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362 </param>
3
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363 <param argument="--custom_weights" type="data" format="safetensors" optional="true" label="Custom Cellpose weights file"/>
2
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364 <section name="channel_map" title="Channel map" expanded="true" help="Specify the channel map for the segmentation task with the corresponding task input data">
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365 <conditional name="channel_red_conditional">
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366 <param name="red" type="select" label="The stain that will be used for red channel">
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367 <expand macro="channel_options_none"/>
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diff changeset
368 </param>
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369 <expand macro="channel_map_conditional_childs"/>
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370 </conditional>
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371 <conditional name="channel_green_conditional">
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372 <param name="green" type="select" label="The stain that will be used for green channel">
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parents: 1
diff changeset
373 <expand macro="channel_options_none"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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parents: 1
diff changeset
374 </param>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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diff changeset
375 <expand macro="channel_map_conditional_childs"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
376 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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diff changeset
377 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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378 <param name="blue" type="select" label="The stain that will be used for blue channel">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
379 <expand macro="channel_options_none"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
380 </param>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
381 <expand macro="channel_map_conditional_childs"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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382 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
383 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
384 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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385 <section name="segmentation_parameters" title="Segmentation parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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386 <param name="nuclear_channel" type="select" label="Nuclear channel">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
387 <expand macro="channel_options_none">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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388 <option value="all">all</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
389 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
390 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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391 <param name="entity_fill_channel" type="select" label="Entity fill channel">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
392 <expand macro="channel_options_none">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
393 <option value="all">all</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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394 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
395 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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396 <param name="diameter" type="integer" min="0" value="30" label="Diameter" help="A default value of 0 automatically estimate the diameter with Cellpose. Too small diameter leads to fragmented cells and too big one leads to over-merged cells"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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397 <param name="flow_threshold" type="float" min="0" max="1" value="0.4" label="Flow threshold" help="Maximum allowed error of the flows for each mask. Increase if cellpose is not returning as many ROIs as you’d expect, and decrease if cellpose is returning too many ill-shaped ROIs"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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398 <param name="cellprob_threshold" type="float" min="-6" max="6" value="0.0" label="Cellprobe threshold" help="Decrease this threshold if cellpose is not returning as many ROIs as you’d expect. Similarly, increase this threshold if cellpose is returning too ROIs particularly from dim areas."/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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399 <param name="minimum_mask_size" type="integer" min="-1" value="15" label="Minimum number of pixels per mask" help="This can be turned off with -1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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400 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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401 <section name="polygon_parameters" title="Polygon parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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402 <param name="simplification_tol" type="integer" min="0" value="2" label="Simplification tolerance" help="The acceptable loss of precision when simplifying cell boundaries. Even a small amount of simplification (2 px) dramatically improves processing time" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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403 <param name="smoothing_radius" type="integer" min="0" value="10" label="Smoothing radius" help="The size of a smoothing operation comparable to morphologically closing and then opening the cell mask using the same structuring element" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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404 <param name="minimum_final_area" type="integer" min="0" value="500" label="Minimum final area" help="Minimum area of a polygon to retain the cell. Used to filter spurious detections." />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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405 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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406 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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407 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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408 <section name="segmentation_task_fusion" title="Segmentation task fusion" help="Specify how the geometries produced by each segmentation task should be combined">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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409 <param name="entity_fusion_strategy" type="select" label="Entity fusion strategy">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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410 <option value="harmonize" selected="true">harmonize (recommended)</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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411 <option value="union">union</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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412 <option value="larger">larger</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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413 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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414 <param name="min_distance_between_entities" type="integer" min="0" value="2" label="Minimum distance between entities" help="When polygons are subtracted from one another, the space between the cells is zero. In order to provide some separation between cells, a minimum distance between these cell can be specified."/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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415 <param name="min_final_area" type="integer" min="0" value="0" label="Minimum area" help="After polygon subtraction, cells smaller than this threshold will be removed"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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416 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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417 <section name="output_files" title="Output files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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418 <param name="entity_types_output" type="select" label="Output entity types">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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419 <option value="cell">cell</option>
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420 <option value="nucleus">nucleus</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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421 <option value="both">both</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
422 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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423 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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424 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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425 <section name="qc_params" title="QC metrics parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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426 <param argument="--experiment-name" type="text" value="Analysis Timestamp" label="The name of the experiment to be used as the index in the output csv and segmentation report">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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427 <sanitizer invalid_char="">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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428 <valid initial="string.letters,string.digits">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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429 <add value="_" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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430 </valid>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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431 </sanitizer>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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432 <validator type="regex">[0-9a-zA-Z_]+</validator>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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433 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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434 <param argument="--input-z-index" type="integer" min="0" value="2" label="The Z plane of the mosaic tiff images to use for the patch"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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435 <param argument="--transcript-count-filter-threshold" type="integer" min="0" value="100" label="The cell transcript count threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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436 <param argument="--volume-filter-threshold" type="integer" min="0" value="200" label="The cell volume threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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437 <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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438 <expand macro="channel_options_none"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
439 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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440 <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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441 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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442 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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443 <option value="DAPI">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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444 <option value="PolyT" selected="true">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
445 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
446 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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447 <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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448 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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449 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
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450 <option value="DAPI" selected="true">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
451 <option value="PolyT">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
452 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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453 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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454 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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455 <expand macro="advanced_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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456 </inputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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457 <outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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458 <collection name="vpt_results" type="list" label="${tool.name} on ${on_string}: VPT Results">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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459 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="csv" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
460 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
461 <collection name="vpt_boundaries" type="list" label="${tool.name} on ${on_string}: VPT segmentation boundaries">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
462 <discover_datasets pattern="(?P&lt;name&gt;.+)\.parquet$" format="parquet" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
463 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
464 <data name="vpt_qc" format="html" from_work_dir="output/metrics.html" label="${tool.name} on ${on_string}: VPT QC"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
465 <collection name="vpt_config_out" type="list" label="${tool.name} on ${on_string}: VPT Config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
466 <discover_datasets pattern="(?P&lt;name&gt;.+)\.json$" format="json" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
467 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
468 <expand macro="common_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
469 </outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
470 <tests>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
471 <!-- test 1: one segmentation task -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
472 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
473 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
474 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
475 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
476 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
477 <section name="experiment_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
478 <param name="z_positions_um" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
479 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
480 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
481 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
482 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
483 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
484 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
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485 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
486 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
487 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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diff changeset
488 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
489 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
490 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
491 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
492 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
493 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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diff changeset
494 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
495 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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diff changeset
496 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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diff changeset
497 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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498 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
499 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
500 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
501 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
502 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
503 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
504 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
505 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
506 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
507 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
508 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
509 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
510 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
511 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
512 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
513 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
514 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
515 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
516 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
517 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
518 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
519 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
520 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
521 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
522 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
523 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
524 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
525 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
526 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
527 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
528 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
529 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
530 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
531 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
532 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
533 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
534 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
535 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
536 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
537 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
538 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
539 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
540 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
541 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
542 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
543 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
544 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
545 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
546 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
547 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
548 <param name="experiment_name" value="cyto2_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
549 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
550 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
551 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
552 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
553 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
554 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
555 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
556 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
557 <has_text_matching expression="0,2,0,3,0,0,0,0,2,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
558 <has_text_matching expression="3,6,3,2,1,3,3,1,3,16,0,8,113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
559 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
560 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
561 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
562 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
563 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
564 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
565 <has_text_matching expression=",777.13824141[0-9]+,70.4487975801[0-9]+,1.976992703078[0-9]+,65.5065863409[0-9]+,"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
566 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
567 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
568 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
569 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
570 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
571 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
572 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
573 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
574 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
575 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
576 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
577 <has_text_matching expression=",Cell count,Cell volume"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
578 <has_n_lines n="3"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
579 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
580 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
581 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
582 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
583 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
584 <has_text_matching expression="813229843.0,4955524.23422[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
585 <has_text_matching expression="587668405.0,22623235.0759[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
586 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
587 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
588 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
589 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
590 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
591 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
592 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
593 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
594 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
595 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
596 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
597 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
598 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
599 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
600 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
601 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
602 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
603 <has_text text="VPT Segmentation Report (cyto2_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
604 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;814&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
605 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;654.0&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
606 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
607 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
608 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
609 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
610 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
611 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
612 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
613 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
614 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
615 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
616 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
617 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
618 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
619 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
620 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
621 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
622 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
623 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
624 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
625 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
626 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
627 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
628 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
629 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
630 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
631 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
632 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
633 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
634 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
635 <!-- test 2: two segmentation tasks -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
636 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
637 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
638 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
639 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
640 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
641 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
642 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
643 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
644 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
645 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
646 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
647 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
648 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
649 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
650 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
651 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
652 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
653 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
654 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
655 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
656 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
657 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
658 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
659 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
660 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
661 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
662 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
663 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
664 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
665 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
666 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
667 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
668 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
669 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
670 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
671 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
672 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
673 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
674 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
675 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
676 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
677 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
678 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
679 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
680 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
681 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
682 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
683 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
684 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
685 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
686 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
687 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
688 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
689 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
690 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
691 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
692 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
693 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
694 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
695 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
696 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
697 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
698 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
699 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
700 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
701 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
702 <param name="model" value="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
703 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
704 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
705 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
706 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
707 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
708 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
709 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
710 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
711 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
712 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
713 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
714 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
715 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
716 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
717 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
718 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
719 <param name="nuclear_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
720 <param name="entity_fill_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
721 <param name="diameter" value="55"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
722 <param name="flow_threshold" value="0.8"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
723 <param name="cellprob_threshold" value="-3.0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
724 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
725 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
726 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
727 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
728 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
729 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
730 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
731 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
732 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
733 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
734 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
735 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
736 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
737 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
738 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
739 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
740 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
741 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
742 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
743 <param name="experiment_name" value="cyto2_2task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
744 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
745 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
746 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
747 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
748 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
749 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
750 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
751 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
752 <has_text_matching expression="0,0,0,0,0,0,0,0,0,1,0,1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
753 <has_text_matching expression="1,2,0,1,2,1,3,0,3,8,0,4,18,2,1,2,2,0,0,2,1,0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
754 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
755 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
756 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
757 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
758 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
759 <has_text_matching expression=",833.754893427[0-9]+,340.820612890[0-9]+,1.070367649097[0-9]+,334.8351650026[0-9]+,-3.129014413402[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
760 <has_text_matching expression=",879.995798798[0-9]+,357.422829969[0-9]+,2.811753148503[0-9]+,352.3315077075[0-9]+,-2.496679594480[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
761 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
762 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
763 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
764 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
765 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
766 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
767 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
768 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
769 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
770 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
771 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
772 <has_text_matching expression=",Cell count,Cell volume"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
773 <has_n_lines n="3"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
774 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
775 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
776 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
777 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
778 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
779 <has_text_matching expression="56353541.0,781480.649952[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
780 <has_text_matching expression="53118509.0,808077.377016[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
781 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
782 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
783 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
784 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
785 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
786 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
787 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
788 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
789 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
790 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
791 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
792 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
793 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
794 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
795 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
796 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
797 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
798 <has_text text="VPT Segmentation Report (cyto2_2task)"/>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
799 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
800 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
801 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
802 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
803 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
804 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
805 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
806 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
807 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
808 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
809 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
810 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
811 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
812 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
813 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
814 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
815 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
816 <has_text_matching expression="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
817 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
818 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
819 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
820 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
821 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
822 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
823 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
824 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
825 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
826 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
827 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
828 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
829 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
830 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
831 <!-- test 3: one segmentation task with custom weight -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
832 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
833 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
834 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
835 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
836 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
837 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
838 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
839 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
840 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
841 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
842 <param name="model" value="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
843 <param name="model_dimensions" value="2D"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
844 <param name="custom_weights" location="https://zenodo.org/records/16784480/files/CP_20230830_093420.safetensors"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
845 <section name="channel_map">
2
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
846 <conditional name="channel_red_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
847 <param name="red" value="Cellbound1"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
848 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
849 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
850 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
851 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
852 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
853 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
854 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
855 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
856 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
857 <conditional name="channel_green_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
858 <param name="green" value="Cellbound3"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
859 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
860 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
861 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
862 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
863 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
864 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
865 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
866 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
867 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
868 <conditional name="channel_blue_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
869 <param name="blue" value="DAPI"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
870 <conditional name="normalize_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
871 <param name="normalize_select" value="Yes"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
872 <conditional name="normalize_type_conditional">
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
873 <param name="normalization" value="CLAHE"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
874 <param name="clip_limit" value="0.01"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
875 <param name="filter_size" value="100"/>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
876 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
877 </conditional>
a88a1e78702e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents: 1
diff changeset
878 </conditional>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
879 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
880 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
881 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
882 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
883 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
884 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
885 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
886 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
887 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
888 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
889 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
890 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
891 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
892 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
893 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
894 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
895 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
896 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
897 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
898 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
899 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
900 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
901 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
902 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
903 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
904 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
905 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
906 <param name="experiment_name" value="custom_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
907 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
908 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
909 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
910 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
911 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
912 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
913 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
914 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
915 <has_text_matching expression="6,10,4,0,5,2,1,0,1,2"/>
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
916 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4,0"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
917 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
918 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
919 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
920 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
921 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
922 <has_text_matching expression="167.0695914980[0-9]+,246.371389688[0-9]+,-1.502969079760[0-9]+,243.9322371166[0-9]+"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
923 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
924 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
925 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
926 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
927 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
928 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
929 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
930 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
931 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
932 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
933 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
934 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
935 <has_text_matching expression=",Cell count,Cell volume"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
936 <has_n_lines n="3"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
937 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
938 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
939 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
940 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
941 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
942 <has_text_matching expression="72859278.0,1502895.008866[0-9]+"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
943 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
944 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
945 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
946 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
947 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
948 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
949 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
950 <has_size size="375308" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
951 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
952 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
953 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
954 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
955 <has_size size="365132" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
956 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
957 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
958 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
959 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
960 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
961 <has_text text="VPT Segmentation Report (custom_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
962 <has_text_matching expression="Cell count: &lt;b class=&quot;summary__value&quot;&gt;93[0-9]+&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
963 <has_text_matching expression="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;49\d*(\.\d+)?&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
964 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
965 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
966 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
967 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
968 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
969 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
970 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
971 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
972 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
973 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
974 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
975 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
976 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
977 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
978 <has_text_matching expression="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
979 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
980 <has_text_matching expression="harmonize"/>
3
0811613196a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f
bgruening
parents: 2
diff changeset
981 <has_text_matching expression="input/model/custom_weights_0.pth"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
982 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
983 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
984 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
985 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
986 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
987 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
988 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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989 <has_text_matching expression="Sum signals finished"/>
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990 <has_text_matching expression="Generate segmentation metrics finished"/>
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991 </assert_contents>
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992 </output>
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993 </test>
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994 </tests>
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995 <help>
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996 The Vizgen Post-processing Tool (VPT) is a scalable and reproducible tool which enables users to reprocess and refine the single-cell results of MERSCOPE experiments.
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997
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998 The **Vizgen Post-processing Tool - Segment Cells** performes **run_segmentation**, **partition_transcripts**, **sum_signals**, **derive-entity-metadata**, and **generate-segmentation-metrics** of the VPT pipeline. The segmentation
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999
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1000 Segmentation parameters for CellPose can be assigned with "**Segmentation configuration file**".
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1001
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1002 The segmentation parameters describes a series of steps to perform on the input data. Using the same segmentation algorithm on a series of experiments ensures that they are processed identically and reproducibly.
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1003
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1004 The segmentation parameters has 3 main sections:
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1005
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1006 1. **Experiment properties**:
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1007 - Holds descriptions of the way the data was collected. Specifically, it must contain a list of the z-indexes and z-positions in the data. This data is used to apply 2D segmentation to 3D data and calculate distances on the z-axis.
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1008 2. **Segmentation tasks**:
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1009 - Holds a list of segmentation tasks to perform. These tasks will be performed sequentially. By running different segmentation tools in "tasks" and combining their output, it is possible to improve cell detection. For example, combining the results of CellPose with the `cyto2` model and the `nuclei` model can dramatically improve the segmentation F1 score over either method alone.
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1010 3. **Segmentation task fusion**:
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1011 - Specifies how the geometries produced by each segmentation task should be combined. All `segmentation_task_fusion` options will produce a non-overlapping set of valid geometries.
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1012 4. **Output files**:
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1013 - Specifies which entity types should be written to disk in the output folder and the file names they should receive.
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1014
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1015
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1016 For more information on the VPT pipeline, please refer to the `VPT user guide`_
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1017
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1018 -----
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1019
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1020 If you want to use a custom-trained model, set the CellPose model to null and provide the custom weights file.
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1021
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1022
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1023 .. class:: infomark
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1024
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1025 **Note:** VPT only supports **9** tasks in a single segmentation algorithm. If more tasks are needed, users are encouraged to run vpt multiple times and combine the segmentation outputs post hoc.
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1026
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1027 .. class:: infomark
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1028
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1029 **Note:** VPT tool on Galaxy only uses **CellPose** algorithm for cell segmentation.
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1030
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1031 .. _`VPT user guide`: https://vizgen.github.io/vizgen-postprocessing/
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1032 </help>
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1033 <expand macro="citations" />
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1034 </tool>