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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
author bgruening
date Sun, 22 Jun 2025 12:25:34 +0000
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8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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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" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @CMD@
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10 ln -s '$detected_transcripts' 'input/detected_transcripts.csv' &&
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11 ln -s '$vpt_config_file' 'input/vpt_config_file.json' &&
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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12 ### segmentation
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13 vpt
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14 @COMMON_ARGS@
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15 run-segmentation
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16 --segmentation-algorithm 'input/vpt_config_file.json'
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17 --input-images 'input/images/'
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18 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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19 --output-path 'output/'
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20 --tile-size $tile_size
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21 #if $max_row_group_size:
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22 --max-row-group-size $max_row_group_size
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23 #end if
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24 --tile-overlap $tile_overlap &&
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25 ### counting partition transcripts
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26 vpt
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27 @COMMON_ARGS@
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28 partition-transcripts
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29 --input-boundaries 'output/cellpose2_micron_space.parquet'
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30 --input-transcripts 'input/detected_transcripts.csv'
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31 --output-entity-by-gene 'output/cell_by_gene.csv'
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32 --output-transcripts 'output/detected_transcripts.csv' &&
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33 ### sum signals
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34 vpt
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35 @COMMON_ARGS@
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36 sum-signals
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37 --input-images 'input/images/'
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38 --input-boundaries 'output/cellpose2_micron_space.parquet'
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39 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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40 --output-csv 'output/sum_signals.csv' &&
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41 ### derive entity metadata
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42 vpt
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43 @COMMON_ARGS@
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44 derive-entity-metadata
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45 --input-boundaries 'output/cellpose2_micron_space.parquet'
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46 --input-entity-by-gene 'output/cell_by_gene.csv'
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47 --output-metadata 'output/cell_metadata.csv' &&
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48 ### segmentation QC
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49 vpt
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50 @COMMON_ARGS@
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51 generate-segmentation-metrics
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52 --input-entity-by-gene 'output/cell_by_gene.csv'
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53 --input-metadata 'output/cell_metadata.csv'
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54 --input-transcripts 'output/detected_transcripts.csv'
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55 --input-boundaries 'output/cellpose2_micron_space.parquet'
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56 --input-micron-to-mosaic 'input/micron_to_mosaic_pixel_transform.csv'
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57 --input-images 'input/images/'
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58 --experiment-name '$qc_params.experiment_name'
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59 --input-z-index '$qc_params.input_z_index'
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60 #if $qc_params.red_stain_name != "None":
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61 --red-stain-name '$qc_params.red_stain_name'
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62 #end if
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63 #if $qc_params.green_stain_name != "None":
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64 --green-stain-name '$qc_params.green_stain_name'
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65 #end if
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66 #if $qc_params.blue_stain_name != "None":
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67 --blue-stain-name '$qc_params.blue_stain_name'
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68 #end if
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69 --transcript-count-filter-threshold '$qc_params.transcript_count_filter_threshold'
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70 --volume-filter-threshold '$qc_params.volume_filter_threshold'
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71 --output-csv 'output/metrics.csv'
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72 --output-report 'output/metrics.html'
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73 --output-clustering 'output/metrics_clustering.parquet' &&
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74 mv 'input/vpt_config_file.json' 'output/vpt_config_file.json'
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75 ]]></command>
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76 <configfiles>
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77 <configfile name="vpt_config_file"><![CDATA[
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78 {
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79 "experiment_properties": {
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80 #set $indices = ",".join([str(i) for i in range(len(str($vpt_config.experiment_properties.z_positions_um.value).split(",")))])
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81
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82 "all_z_indexes": [$indices],
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83 "z_positions_um": [$vpt_config.experiment_properties.z_positions_um]
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84 },
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85 "segmentation_tasks": [
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86 #set $task_n = len($vpt_config.segmentation_tasks.segmentation_task) - 1
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87 #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
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88 {
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89 "task_id": $i,
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90 "segmentation_family": "Cellpose2",
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91 #if $task.entity_types_detected != "both":
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92 "entity_types_detected": ["$task.entity_types_detected"],
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93 #else:
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94 "entity_types_detected": [
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95 "nuclei",
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96 "cell"
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97 ],
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98 #end if
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99 "z_layers": [$task.z_layers],
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100 "segmentation_properties": {
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101 #if $task.segmentation_properties.model != "null":
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102 "model": "$task.segmentation_properties.model",
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103 #else:
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104 "model": null,
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105 #end if
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106 "model_dimensions": "$task.segmentation_properties.model_dimensions",
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107 #if $task.segmentation_properties.custom_weights:
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108 "custom_weights": "$task.segmentation_properties.custom_weights",
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109 #else:
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110 "custom_weights": null,
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111 #end if
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112 "channel_map": {
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113 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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114 "red": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
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115 #else:
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116 "red": "",
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117 #end if
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118 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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119 "green": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
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120 #else:
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121 "green": "",
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122 #end if
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123 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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124 "blue": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue"
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125 #else:
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126 "blue": ""
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127 #end if
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128 }
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129 },
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130 "task_input_data": [
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131 #if $task.segmentation_properties.channel_map.channel_red_conditional.red != "None":
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132 #set $input_data = $task.segmentation_properties.channel_map.channel_red_conditional
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133 {
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134 "image_channel": "$task.segmentation_properties.channel_map.channel_red_conditional.red",
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135 "image_preprocessing": [
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136 #if $input_data.normalize_conditional.normalize_select == "Yes":
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137 {
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138 "name": "normalize",
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139 "parameters": {
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140 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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141 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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142 "filter_size": [
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143 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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144 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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145 ],
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146 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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147 #end if
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148 }
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149 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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150 ,
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151 #end if
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152 #end if
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153 #if $input_data.blur_conditional.blur_select == "Yes":
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154 {
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155 "name": "blur",
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156 "parameters": {
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157 "type": "$input_data.blur_conditional.blur_options",
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158 "size": $input_data.blur_conditional.kernel_size
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159 }
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160 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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161 ,
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162 #end if
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163 #end if
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164 #if $input_data.downsample_conditional.downsample_select == "Yes":
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165 {
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166 "name": "downsample",
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167 "parameters": {
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168 "scale": "$input_data.downsample_conditional.scale"
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169 }
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170 }
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171 #end if
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172 ]
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173 }#if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None" or $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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174 ,
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175 #end if
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176 #end if
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177 #if $task.segmentation_properties.channel_map.channel_green_conditional.green != "None":
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178 #set $input_data = $task.segmentation_properties.channel_map.channel_green_conditional
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179 {
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180 "image_channel": "$task.segmentation_properties.channel_map.channel_green_conditional.green",
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181 "image_preprocessing": [
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182 #if $input_data.normalize_conditional.normalize_select == "Yes":
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183 {
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184 "name": "normalize",
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185 "parameters": {
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186 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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187 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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188 "filter_size": [
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189 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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190 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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191 ],
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192 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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193 #end if
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194 }
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195 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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196 ,
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197 #end if
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198 #end if
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199 #if $input_data.blur_conditional.blur_select == "Yes":
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200 {
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201 "name": "blur",
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202 "parameters": {
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203 "type": "$input_data.blur_conditional.blur_options",
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204 "size": $input_data.blur_conditional.kernel_size
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205 }
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206 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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207 ,
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208 #end if
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209 #end if
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210 #if $input_data.downsample_conditional.downsample_select == "Yes":
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211 {
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212 "name": "downsample",
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213 "parameters": {
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214 "scale": "$input_data.downsample_conditional.scale"
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215 }
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216 }
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217 #end if
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218 ]
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219 }#if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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220 ,
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221 #end if
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222 #end if
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223 #if $task.segmentation_properties.channel_map.channel_blue_conditional.blue != "None":
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224 #set $input_data = $task.segmentation_properties.channel_map.channel_blue_conditional
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225 {
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226 "image_channel": "$task.segmentation_properties.channel_map.channel_blue_conditional.blue",
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227 "image_preprocessing": [
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228 #if $input_data.normalize_conditional.normalize_select == "Yes":
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229 {
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230 "name": "normalize",
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231 "parameters": {
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232 #if $input_data.normalize_conditional.normalize_type_conditional.normalization == "CLAHE":
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233 "clip_limit": $input_data.normalize_conditional.normalize_type_conditional.clip_limit,
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234 "filter_size": [
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235 $input_data.normalize_conditional.normalize_type_conditional.filter_size,
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236 $input_data.normalize_conditional.normalize_type_conditional.filter_size
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237 ],
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238 "type": "$input_data.normalize_conditional.normalize_type_conditional.normalization"
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239 #end if
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240 }
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241 }#if $input_data.blur_conditional.blur_select == "Yes" or $input_data.downsample_conditional.downsample_select == "Yes"
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242 ,
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243 #end if
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244 #end if
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245 #if $input_data.blur_conditional.blur_select == "Yes":
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246 {
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247 "name": "blur",
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248 "parameters": {
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249 "type": "$input_data.blur_conditional.blur_options",
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250 "size": $input_data.blur_conditional.kernel_size
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251 }
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252 }#if $input_data.downsample_conditional.downsample_select == "Yes"
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253 ,
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254 #end if
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255 #end if
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256 #if $input_data.downsample_conditional.downsample_select == "Yes":
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257 {
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258 "name": "downsample",
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259 "parameters": {
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260 "scale": "$input_data.downsample_conditional.scale"
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261 }
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262 }
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263 #end if
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264 ]
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265 }
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266 #end if
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267 ],
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268 "segmentation_parameters": {
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269 #if $task.segmentation_parameters.nuclear_channel != "None":
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270 "nuclear_channel": "$task.segmentation_parameters.nuclear_channel",
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271 #else:
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272 "nuclear_channel": null,
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273 #end if
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274 #if $task.segmentation_parameters.entity_fill_channel != "None":
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275 "entity_fill_channel": "$task.segmentation_parameters.entity_fill_channel",
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276 #else:
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277 "entity_fill_channel": null,
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278 #end if
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279 "diameter": $task.segmentation_parameters.diameter,
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280 "flow_threshold": $task.segmentation_parameters.flow_threshold,
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281 "cellprob_threshold": $task.segmentation_parameters.cellprob_threshold,
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282 "minimum_mask_size": $task.segmentation_parameters.minimum_mask_size
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283 },
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284 "polygon_parameters": {
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285 "simplification_tol": $task.polygon_parameters.simplification_tol,
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286 "smoothing_radius": $task.polygon_parameters.smoothing_radius,
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287 "minimum_final_area": $task.polygon_parameters.minimum_final_area
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288 }
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289 }#if $i != $task_n
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290 ,
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291 #end if
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292 #end for
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293 ],
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294 "segmentation_task_fusion": {
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295 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
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296 "fused_polygon_postprocessing_parameters": {
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297 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities,
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298 "min_final_area": $segmentation_task_fusion.min_final_area
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299 }
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300 },
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301 "output_files": [
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302 {
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303 #if $vpt_config.output_files.entity_types_output != "both":
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304 "entity_types_output": ["$vpt_config.output_files.entity_types_output"],
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305 #else:
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306 "entity_types_output": [
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307 "nuclei",
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308 "cell"
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309 ],
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310 #end if
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311 "files": {
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312 "run_on_tile_dir": "result_tiles/",
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313 "mosaic_geometry_file": "cellpose2_mosaic_space.parquet",
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314 "micron_geometry_file": "cellpose2_micron_space.parquet",
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315 "cell_metadata_file": "cellpose2_cell_metadata.csv"
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316 }
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317 }
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318 ]
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319 }
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320 ]]></configfile>
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321 </configfiles>
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322 <inputs>
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323 <expand macro="common_input"/>
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324 <param argument="--detected_transcripts" type="data" format="csv" label="Detected transcripts"/>
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325 <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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326 <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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327 <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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328 <section name="vpt_config" title="Segmentation configuration file">
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329 <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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330 <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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331 <expand macro="sanitize_digits"/>
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332 </param>
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333 </section>
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334 <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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335 <repeat name="segmentation_task" min="1" max="9" title="Segmentation tasks">
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336 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?">
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337 <option value="cell">cell</option>
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338 <option value="nucleus">nucleus</option>
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339 <option value="both">both</option>
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340 </param>
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341 <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
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342 <expand macro="sanitize_digits"/>
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343 </param>
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344 <section name="segmentation_properties" title="Segmentation properties">
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345 <param argument="--model" type="select" label="Cellpose model">
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346 <option value="cyto2">cyto2</option>
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347 <option value="nuclei">nuclei</option>
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348 <option value="null">null</option>
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349 </param>
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350 <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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351 <option value="2D">2D</option>
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352 <option value="3D">3D</option>
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353 </param>
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354 <param argument="--custom_weights" type="data" format="data" optional="true" label="Custom Cellpose weights file"/>
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355 <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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356 <conditional name="channel_red_conditional">
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357 <param name="red" type="select" label="The stain that will be used for red channel">
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358 <expand macro="channel_options_none"/>
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359 </param>
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360 <expand macro="channel_map_conditional_childs"/>
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361 </conditional>
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362 <conditional name="channel_green_conditional">
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363 <param name="green" type="select" label="The stain that will be used for green channel">
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364 <expand macro="channel_options_none"/>
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365 </param>
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366 <expand macro="channel_map_conditional_childs"/>
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367 </conditional>
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368 <conditional name="channel_blue_conditional">
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369 <param name="blue" type="select" label="The stain that will be used for blue channel">
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370 <expand macro="channel_options_none"/>
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371 </param>
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372 <expand macro="channel_map_conditional_childs"/>
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373 </conditional>
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374 </section>
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375 </section>
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376 <section name="segmentation_parameters" title="Segmentation parameters">
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377 <param name="nuclear_channel" type="select" label="Nuclear channel">
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378 <expand macro="channel_options_none">
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379 <option value="all">all</option>
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380 </expand>
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381 </param>
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382 <param name="entity_fill_channel" type="select" label="Entity fill channel">
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383 <expand macro="channel_options_none">
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384 <option value="all">all</option>
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385 </expand>
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386 </param>
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387 <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"/>
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388 <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"/>
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389 <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."/>
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390 <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"/>
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391 </section>
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392 <section name="polygon_parameters" title="Polygon parameters">
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393 <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" />
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394 <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" />
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395 <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." />
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396 </section>
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397 </repeat>
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398 </section>
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399 <section name="segmentation_task_fusion" title="Segmentation task fusion" help="Specify how the geometries produced by each segmentation task should be combined">
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400 <param name="entity_fusion_strategy" type="select" label="Entity fusion strategy">
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401 <option value="harmonize" selected="true">harmonize (recommended)</option>
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402 <option value="union">union</option>
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403 <option value="larger">larger</option>
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404 </param>
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405 <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."/>
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406 <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"/>
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407 </section>
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408 <section name="output_files" title="Output files">
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409 <param name="entity_types_output" type="select" label="Output entity types">
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410 <option value="cell">cell</option>
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411 <option value="nucleus">nucleus</option>
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412 <option value="both">both</option>
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413 </param>
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414 </section>
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415 </section>
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416 <section name="qc_params" title="QC metrics parameters">
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417 <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">
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418 <sanitizer invalid_char="">
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419 <valid initial="string.letters,string.digits">
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420 <add value="_" />
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421 </valid>
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422 </sanitizer>
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423 <validator type="regex">[0-9a-zA-Z_]+</validator>
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424 </param>
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425 <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"/>
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426 <param argument="--transcript-count-filter-threshold" type="integer" min="0" value="100" label="The cell transcript count threshold used for computing metrics and clustering"/>
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427 <param argument="--volume-filter-threshold" type="integer" min="0" value="200" label="The cell volume threshold used for computing metrics and clustering"/>
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428 <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel in images">
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429 <expand macro="channel_options_none"/>
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430 </param>
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431 <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel in images">
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432 <expand macro="channel_options_basic">
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433 <option value="None">None</option>
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434 <option value="DAPI">DAPI</option>
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435 <option value="PolyT" selected="true">PolyT</option>
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436 </expand>
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437 </param>
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438 <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel in images">
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439 <expand macro="channel_options_basic">
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440 <option value="None">None</option>
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441 <option value="DAPI" selected="true">DAPI</option>
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442 <option value="PolyT">PolyT</option>
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443 </expand>
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444 </param>
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445 </section>
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446 <expand macro="advanced_output"/>
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447 </inputs>
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448 <outputs>
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449 <collection name="vpt_results" type="list" label="${tool.name} on ${on_string}: VPT Results">
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450 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="csv" directory="output"/>
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451 </collection>
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452 <collection name="vpt_boundaries" type="list" label="${tool.name} on ${on_string}: VPT segmentation boundaries">
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453 <discover_datasets pattern="(?P&lt;name&gt;.+)\.parquet$" format="parquet" directory="output"/>
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454 </collection>
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455 <data name="vpt_qc" format="html" from_work_dir="output/metrics.html" label="${tool.name} on ${on_string}: VPT QC"/>
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456 <collection name="vpt_config_out" type="list" label="${tool.name} on ${on_string}: VPT Config">
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457 <discover_datasets pattern="(?P&lt;name&gt;.+)\.json$" format="json" directory="output"/>
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458 </collection>
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459 <expand macro="common_output"/>
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460 </outputs>
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461 <tests>
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462 <!-- test 1: one segmentation task -->
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463 <test expect_num_outputs="5">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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464 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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465 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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466 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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467 <section name="vpt_config">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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468 <section name="experiment_properties">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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469 <param name="z_positions_um" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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470 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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471 <section name="segmentation_tasks">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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472 <repeat name="segmentation_task">
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473 <param name="entity_types_detected" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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474 <param name="z_layers" value="3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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475 <section name="segmentation_properties">
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476 <param name="model" value="cyto2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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477 <param name="model_dimensions" value="2D"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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478 <section name="channel_map">
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479 <conditional name="channel_red_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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480 <param name="red" value="Cellbound1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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481 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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482 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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483 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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484 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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485 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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486 <param name="filter_size" value="100"/>
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487 </conditional>
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488 </conditional>
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489 </conditional>
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490 <conditional name="channel_green_conditional">
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491 <param name="green" value="Cellbound3"/>
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492 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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493 <param name="normalize_select" value="Yes"/>
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494 <conditional name="normalize_type_conditional">
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495 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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496 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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497 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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498 </conditional>
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499 </conditional>
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500 </conditional>
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501 <conditional name="channel_blue_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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502 <param name="blue" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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503 <conditional name="normalize_conditional">
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504 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
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505 <conditional name="normalize_type_conditional">
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506 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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diff changeset
507 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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508 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
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diff changeset
509 </conditional>
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510 </conditional>
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511 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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512 </section>
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513 </section>
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514 <section name="segmentation_parameters">
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515 <param name="nuclear_channel" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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516 <param name="entity_fill_channel" value="all"/>
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517 <param name="diameter" value="70"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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518 <param name="flow_threshold" value="0.95"/>
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519 <param name="cellprob_threshold" value="-5.5"/>
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520 <param name="minimum_mask_size" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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diff changeset
521 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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522 <section name="polygon_parameters">
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523 <param name="simplification_tol" value="2"/>
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diff changeset
524 <param name="smoothing_radius" value="10"/>
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525 <param name="minimum_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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diff changeset
526 </section>
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527 </repeat>
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528 </section>
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529 <section name="segmentation_task_fusion">
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530 <param name="entity_fusion_strategy" value="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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parents:
diff changeset
531 <param name="min_distance_between_entities" value="1"/>
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532 <param name="min_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
533 </section>
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bgruening
parents:
diff changeset
534 <section name="output_files">
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535 <param name="entity_types_output" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
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536 </section>
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537 </section>
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538 <section name="qc_params">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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539 <param name="experiment_name" value="cyto2_1task"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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540 </section>
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541 <section name="advanced_output">
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542 <param name="log" value="true"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
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543 </section>
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544 <output_collection name="vpt_results" type="list">
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diff changeset
545 <element name="cell_by_gene">
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546 <assert_contents>
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diff changeset
547 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
548 <has_text_matching expression="0,2,0,3,0,0,0,0,2,6"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
549 <has_text_matching expression="3,6,3,2,1,3,3,1,3,16,0,8,113"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
550 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
551 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
552 <element name="cell_metadata">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
553 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
554 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
555 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
556 <has_text_matching expression=",416.540438981[0-9]+,68.7110642977[0-9]+,9.67291568732[0-9]+,64.4947481953[0-9]+,"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
557 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
558 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
559 <element name="detected_transcripts">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
560 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
561 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
562 <has_text_matching expression="86,10,285.00012,10.13364,0.0,816.0,153.0,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
563 <has_text_matching expression="229,10,274.95612,35.72964,0.0,723.0,390.0,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
564 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
565 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
566 <element name="metrics">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
567 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
568 <has_text_matching expression=",Cell count,Cell volume"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
569 <has_text_matching expression="All cells,814,1572.4,1533.3,735.8,654.0,92.1,108.0,96.4,68.2,0.0"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
570 <has_text_matching expression="Cells after filtering,700,1694.1,1667.9,851.1,810.5,104.5,111.0,95.9,63.2,0.06"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
571 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
572 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
573 <element name="sum_signals">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
574 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
575 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
576 <has_text_matching expression="813229843.0,4955524.23422[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
577 <has_text_matching expression="587668405.0,22623235.0759[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
578 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
579 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
580 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
581 <output_collection name="vpt_boundaries" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
582 <element name="cellpose2_micron_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
583 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
584 <has_size size="232259" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
585 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
586 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
587 <element name="cellpose2_mosaic_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
588 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
589 <has_size size="215395" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
590 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
591 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
592 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
593 <output name="vpt_qc">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
594 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
595 <has_text text="VPT Segmentation Report (cyto2_1task)"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
596 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;814&lt;/b&gt;&lt;/p&gt;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
597 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;654.0&lt;/b&gt;&lt;/p&gt;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
598 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
599 </output>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
600 <output_collection name="vpt_config_out" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
601 <element name="segmentation_specification">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
602 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
603 <has_text_matching expression="input/vpt_config_file.json"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
604 <has_text_matching expression="input/images/"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
605 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
606 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
607 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
608 <element name="vpt_config_file">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
609 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
610 <has_text_matching expression="0,1,2,3,4,5,6"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
611 <has_text_matching expression="Cellpose2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
612 <has_text_matching expression="cyto2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
613 <has_text_matching expression="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
614 <has_text_matching expression="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
615 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
616 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
617 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
618 <output name="vpt_log">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
619 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
620 <has_text_matching expression="run_segmentation finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
621 <has_text_matching expression="Partition transcripts finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
622 <has_text_matching expression="Sum signals finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
623 <has_text_matching expression="Generate segmentation metrics finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
624 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
625 </output>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
626 </test>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
627 <!-- test 2: two segmentation tasks -->
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
628 <test expect_num_outputs="5">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
629 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
630 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
631 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
632 <section name="vpt_config">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
633 <section name="segmentation_tasks">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
634 <repeat name="segmentation_task">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
635 <param name="entity_types_detected" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
636 <param name="z_layers" value="3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
637 <section name="segmentation_properties">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
638 <param name="model" value="cyto2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
639 <param name="model_dimensions" value="2D"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
640 <section name="channel_map">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
641 <conditional name="channel_red_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
642 <param name="red" value="Cellbound1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
643 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
644 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
645 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
646 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
647 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
648 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
649 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
650 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
651 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
652 <conditional name="channel_green_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
653 <param name="green" value="Cellbound3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
654 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
655 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
656 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
657 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
658 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
659 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
660 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
661 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
662 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
663 <conditional name="channel_blue_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
664 <param name="blue" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
665 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
666 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
667 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
668 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
669 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
670 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
671 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
672 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
673 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
674 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
675 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
676 <section name="segmentation_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
677 <param name="nuclear_channel" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
678 <param name="entity_fill_channel" value="all"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
679 <param name="diameter" value="70"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
680 <param name="flow_threshold" value="0.95"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
681 <param name="cellprob_threshold" value="-5.5"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
682 <param name="minimum_mask_size" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
683 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
684 <section name="polygon_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
685 <param name="simplification_tol" value="2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
686 <param name="smoothing_radius" value="10"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
687 <param name="minimum_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
688 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
689 </repeat>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
690 <repeat name="segmentation_task">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
691 <param name="entity_types_detected" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
692 <param name="z_layers" value="3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
693 <section name="segmentation_properties">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
694 <param name="model" value="nuclei"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
695 <param name="model_dimensions" value="2D"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
696 <section name="channel_map">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
697 <conditional name="channel_blue_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
698 <param name="blue" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
699 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
700 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
701 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
702 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
703 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
704 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
705 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
706 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
707 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
708 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
709 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
710 <section name="segmentation_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
711 <param name="nuclear_channel" value="all"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
712 <param name="entity_fill_channel" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
713 <param name="diameter" value="55"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
714 <param name="flow_threshold" value="0.8"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
715 <param name="cellprob_threshold" value="-3.0"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
716 <param name="minimum_mask_size" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
717 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
718 <section name="polygon_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
719 <param name="simplification_tol" value="2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
720 <param name="smoothing_radius" value="10"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
721 <param name="minimum_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
722 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
723 </repeat>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
724 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
725 <section name="segmentation_task_fusion">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
726 <param name="entity_fusion_strategy" value="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
727 <param name="min_distance_between_entities" value="1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
728 <param name="min_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
729 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
730 <section name="output_files">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
731 <param name="entity_types_output" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
732 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
733 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
734 <section name="qc_params">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
735 <param name="experiment_name" value="cyto2_2task"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
736 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
737 <section name="advanced_output">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
738 <param name="log" value="true"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
739 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
740 <output_collection name="vpt_results" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
741 <element name="cell_by_gene">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
742 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
743 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
744 <has_text_matching expression="0,0,0,0,0,0,0,0,0,1,0,1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
745 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
746 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
747 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
748 <element name="cell_metadata">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
749 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
750 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
751 <has_text_matching expression=",833.754893427[0-9]+,340.820612890[0-9]+,1.070367649097[0-9]+,334.8351650026[0-9]+,-3.129014413402[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
752 <has_text_matching expression=",879.995798798[0-9]+,357.422829969[0-9]+,2.811753148503[0-9]+,352.3315077075[0-9]+,-2.496679594480[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
753 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
754 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
755 <element name="detected_transcripts">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
756 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
757 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
758 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
759 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
760 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
761 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
762 <element name="metrics">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
763 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
764 <has_text_matching expression=",Cell count,Cell volume"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
765 <has_text_matching expression="All cells,811,1588.0,1549.9,740.5,669.0,92.2,109.0,96.7,68.6,0.0"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
766 <has_text_matching expression="Cells after filtering,698,1711.6,1705.9,856.1,817.5,104.6,111.0,96.2,63.7,0.06"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
767 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
768 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
769 <element name="sum_signals">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
770 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
771 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
772 <has_text_matching expression="56353541.0,781480.649952[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
773 <has_text_matching expression="53118509.0,808077.377016[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
774 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
775 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
776 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
777 <output_collection name="vpt_boundaries" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
778 <element name="cellpose2_micron_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
779 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
780 <has_size size="232259" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
781 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
782 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
783 <element name="cellpose2_mosaic_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
784 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
785 <has_size size="215395" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
786 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
787 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
788 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
789 <output name="vpt_qc">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
790 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
791 <has_text text="VPT Segmentation Report (cyto2_2task)"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
792 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
793 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
794 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
795 </output>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
796 <output_collection name="vpt_config_out" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
797 <element name="segmentation_specification">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
798 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
799 <has_text_matching expression="input/vpt_config_file.json"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
800 <has_text_matching expression="input/images/"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
801 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
802 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
803 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
804 <element name="vpt_config_file">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
805 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
806 <has_text_matching expression="0,1,2,3,4,5,6"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
807 <has_text_matching expression="Cellpose2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
808 <has_text_matching expression="cyto2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
809 <has_text_matching expression="nuclei"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
810 <has_text_matching expression="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
811 <has_text_matching expression="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
812 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
813 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
814 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
815 <output name="vpt_log">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
816 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
817 <has_text_matching expression="run_segmentation finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
818 <has_text_matching expression="Partition transcripts finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
819 <has_text_matching expression="Sum signals finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
820 <has_text_matching expression="Generate segmentation metrics finished"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
821 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
822 </output>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
823 </test>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
824 <!-- test 3: one segmentation task with custom weight -->
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
825 <test expect_num_outputs="5">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
826 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
827 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
828 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
829 <section name="vpt_config">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
830 <section name="segmentation_tasks">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
831 <repeat name="segmentation_task">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
832 <param name="entity_types_detected" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
833 <param name="z_layers" value="3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
834 <section name="segmentation_properties">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
835 <param name="model" value="null"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
836 <param name="model_dimensions" value="2D"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
837 <param name="custom_weights" location="https://zenodo.org/records/15319018/files/CP_20230830_093420"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
838 <section name="channel_map">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
839 <conditional name="channel_red_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
840 <param name="red" value="Cellbound1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
841 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
842 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
843 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
844 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
845 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
846 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
847 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
848 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
849 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
850 <conditional name="channel_green_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
851 <param name="green" value="Cellbound3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
852 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
853 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
854 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
855 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
856 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
857 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
858 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
859 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
860 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
861 <conditional name="channel_blue_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
862 <param name="blue" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
863 <conditional name="normalize_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
864 <param name="normalize_select" value="Yes"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
865 <conditional name="normalize_type_conditional">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
866 <param name="normalization" value="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
867 <param name="clip_limit" value="0.01"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
868 <param name="filter_size" value="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
869 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
870 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
871 </conditional>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
872 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
873 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
874 <section name="segmentation_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
875 <param name="nuclear_channel" value="DAPI"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
876 <param name="entity_fill_channel" value="all"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
877 <param name="diameter" value="70"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
878 <param name="flow_threshold" value="0.95"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
879 <param name="cellprob_threshold" value="-5.5"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
880 <param name="minimum_mask_size" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
881 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
882 <section name="polygon_parameters">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
883 <param name="simplification_tol" value="2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
884 <param name="smoothing_radius" value="10"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
885 <param name="minimum_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
886 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
887 </repeat>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
888 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
889 <section name="segmentation_task_fusion">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
890 <param name="entity_fusion_strategy" value="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
891 <param name="min_distance_between_entities" value="1"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
892 <param name="min_final_area" value="500"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
893 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
894 <section name="output_files">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
895 <param name="entity_types_output" value="cell"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
896 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
897 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
898 <section name="qc_params">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
899 <param name="experiment_name" value="custom_1task"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
900 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
901 <section name="advanced_output">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
902 <param name="log" value="true"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
903 </section>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
904 <output_collection name="vpt_results" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
905 <element name="cell_by_gene">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
906 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
907 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
908 <has_text_matching expression="6,11,4,0,5,2,1,0,1,2,1,2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
909 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
910 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
911 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
912 <element name="cell_metadata">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
913 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
914 <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"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
915 <has_text_matching expression="168.0683921161[0-9]+,246.3592447472[0-9]+,-1.507707574380[0-9]+,243.9322371166[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
916 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
917 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
918 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
919 <element name="detected_transcripts">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
920 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
921 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
922 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
923 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
924 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
925 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
926 <element name="metrics">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
927 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
928 <has_text_matching expression=",Cell count,Cell volume"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
929 <has_text_matching expression="All cells,93[0-9]+,121\d*(\.\d+)?,118\d*(\.\d+)?,60\d*(\.\d+)?,49\d*(\.\d+)?,7\d*(\.\d+)?,10\d*(\.\d+)?,9\d*(\.\d+)?,6\d*(\.\d+)?,0.0"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
930 <has_text_matching expression="Cells after filtering,659,1532.9,1553.5,850.2,837.0,104.8,112.0,90.2,53.8,0.15"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
931 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
932 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
933 <element name="sum_signals">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
934 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
935 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
936 <has_text_matching expression="73446567.0,1605103.666715[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
937 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
938 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
939 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
940 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
941 <output_collection name="vpt_boundaries" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
942 <element name="cellpose2_micron_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
943 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
944 <has_size size="375308" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
945 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
946 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
947 <element name="cellpose2_mosaic_space">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
948 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
949 <has_size size="365132" delta="100"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
950 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
951 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
952 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
953 <output name="vpt_qc">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
954 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
955 <has_text text="VPT Segmentation Report (custom_1task)"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
956 <has_text_matching expression="Cell count: &lt;b class=&quot;summary__value&quot;&gt;93[0-9]+&lt;/b&gt;&lt;/p&gt;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
957 <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;"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
958 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
959 </output>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
960 <output_collection name="vpt_config_out" type="list">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
961 <element name="segmentation_specification">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
962 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
963 <has_text_matching expression="input/vpt_config_file.json"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
964 <has_text_matching expression="input/images/"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
965 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
966 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
967 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
968 <element name="vpt_config_file">
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
969 <assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
970 <has_text_matching expression="0,1,2,3,4,5,6"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
971 <has_text_matching expression="Cellpose2"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
972 <has_text_matching expression="null"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
973 <has_text_matching expression="CLAHE"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
974 <has_text_matching expression="harmonize"/>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
975 </assert_contents>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
976 </element>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
diff changeset
977 </output_collection>
8b9500115e69 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 16e04b2423dc0380a47243fb15bfd120dd95dedc
bgruening
parents:
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978 <output name="vpt_log">
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979 <assert_contents>
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980 <has_text_matching expression="run_segmentation finished"/>
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981 <has_text_matching expression="Partition transcripts finished"/>
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982 <has_text_matching expression="Sum signals finished"/>
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983 <has_text_matching expression="Generate segmentation metrics finished"/>
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984 </assert_contents>
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985 </output>
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986 </test>
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987 </tests>
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988 <help>
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989 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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990
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991 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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992
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993 Segmentation parameters for CellPose can be assigned with "**Segmentation configuration file**".
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994
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995 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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996
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997 The segmentation parameters has 3 main sections:
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998
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999 1. **Experiment properties**:
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1000 - 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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1001 2. **Segmentation tasks**:
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1002 - 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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1003 3. **Segmentation task fusion**:
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1004 - 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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1005 4. **Output files**:
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1006 - Specifies which entity types should be written to disk in the output folder and the file names they should receive.
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1007
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1008
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1009 For more information on the VPT pipeline, please refer to the `VPT user guide`_
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1010
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1011 -----
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1012
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1013 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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1014
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1015
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1016 .. class:: infomark
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1017
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1018 **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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1019
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1020 .. class:: infomark
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1021
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1022 **Note:** VPT tool on Galaxy only uses **CellPose** algorithm for cell segmentation.
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1023
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1024 .. _`VPT user guide`: https://vizgen.github.io/vizgen-postprocessing/
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1025 </help>
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1026 <expand macro="citations" />
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1027 </tool>