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annotate vpt_segment.xml @ 1:ed28a1feba82 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
author bgruening
date Mon, 26 May 2025 06:54:28 +0000
parents 5bd5f26279fd
children a88a1e78702e
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5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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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' &&
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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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": [
1
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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):
0
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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 $task.segmentation_properties.channel_map.red != "None":
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114 "red": "$task.segmentation_properties.channel_map.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 $task.segmentation_properties.channel_map.green != "None":
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119 "green": "$task.segmentation_properties.channel_map.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 $task.segmentation_properties.channel_map.blue != "None":
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124 "blue": "$task.segmentation_properties.channel_map.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 #set $input_data_n = len($task.task_input_data.task_input) - 1
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132 #for $j, $input_data in enumerate($task.task_input_data.task_input):
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133 {
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134 "image_channel": "$input_data.image_channel",
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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 $j != $input_data_n
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174 ,
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175 #end if
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176 #end for
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177 ],
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178 "segmentation_parameters": {
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179 #if $task.segmentation_parameters.nuclear_channel != "None":
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180 "nuclear_channel": "$task.segmentation_parameters.nuclear_channel",
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181 #else:
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182 "nuclear_channel": null,
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183 #end if
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184 #if $task.segmentation_parameters.entity_fill_channel != "None":
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185 "entity_fill_channel": "$task.segmentation_parameters.entity_fill_channel",
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186 #else:
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187 "entity_fill_channel": null,
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188 #end if
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189 "diameter": $task.segmentation_parameters.diameter,
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190 "flow_threshold": $task.segmentation_parameters.flow_threshold,
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191 "cellprob_threshold": $task.segmentation_parameters.cellprob_threshold,
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192 "minimum_mask_size": $task.segmentation_parameters.minimum_mask_size
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193 },
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194 "polygon_parameters": {
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195 "simplification_tol": $task.polygon_parameters.simplification_tol,
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196 "smoothing_radius": $task.polygon_parameters.smoothing_radius,
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197 "minimum_final_area": $task.polygon_parameters.minimum_final_area
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198 }
1
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199 }#if $i != $task_n
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200 ,
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201 #end if
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202 #end for
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203 ],
0
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204 "segmentation_task_fusion": {
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205 "entity_fusion_strategy": "$segmentation_task_fusion.entity_fusion_strategy",
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206 "fused_polygon_postprocessing_parameters": {
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207 "min_distance_between_entities": $segmentation_task_fusion.min_distance_between_entities,
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208 "min_final_area": $segmentation_task_fusion.min_final_area
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209 }
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210 },
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211 "output_files": [
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212 {
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213 #if $vpt_config.output_files.entity_types_output != "both":
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214 "entity_types_output": ["$vpt_config.output_files.entity_types_output"],
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215 #else:
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216 "entity_types_output": [
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217 "nuclei",
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218 "cell"
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219 ],
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220 #end if
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221 "files": {
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222 "run_on_tile_dir": "result_tiles/",
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223 "mosaic_geometry_file": "cellpose2_mosaic_space.parquet",
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224 "micron_geometry_file": "cellpose2_micron_space.parquet",
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225 "cell_metadata_file": "cellpose2_cell_metadata.csv"
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226 }
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227 }
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228 ]
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229 }
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230 ]]></configfile>
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231 </configfiles>
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232 <inputs>
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233 <expand macro="common_input"/>
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234 <param argument="--detected_transcripts" type="data" format="csv" label="Detected transcripts"/>
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235 <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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236 <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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237 <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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238 <section name="vpt_config" title="Segmentation configuration file">
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239 <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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240 <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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241 <expand macro="sanitize_digits"/>
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242 </param>
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243 </section>
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244 <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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245 <repeat name="segmentation_task" min="1" max="9" title="Segmentation tasks">
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246 <param argument="--entity_types_detected" type="select" label="Detect cell or nucleus?">
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247 <option value="cell">cell</option>
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248 <option value="nucleus">nucleus</option>
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249 <option value="both">both</option>
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250 </param>
1
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251 <param argument="--z_layers" type="text" value="3" optional="false" label="Comma-separated list of z-index images to segment.">
0
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252 <expand macro="sanitize_digits"/>
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253 </param>
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254 <section name="segmentation_properties" title="Segmentation properties">
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255 <param argument="--model" type="select" label="Cellpose model">
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256 <option value="cyto2">cyto2</option>
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257 <option value="nuclei">nuclei</option>
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258 <option value="null">null</option>
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259 </param>
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260 <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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261 <option value="2D">2D</option>
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262 <option value="3D">3D</option>
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263 </param>
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264 <param argument="--custom_weights" type="data" format="data" optional="true" label="Custom Cellpose weights file"/>
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265 <section name="channel_map" title="Channel map">
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266 <param name="red" type="select" label="The stain that will be used for red channel">
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267 <expand macro="channel_options_none"/>
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268 </param>
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269 <param name="green" type="select" label="The stain that will be used for green channel">
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270 <expand macro="channel_options_none"/>
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271 </param>
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272 <param name="blue" type="select" label="The stain that will be used for blue channel">
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273 <expand macro="channel_options_none"/>
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274 </param>
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275 </section>
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276 </section>
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277 <section name="segmentation_parameters" title="Segmentation parameters">
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278 <param name="nuclear_channel" type="select" label="Nuclear channel">
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279 <expand macro="channel_options_none">
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280 <option value="all">all</option>
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281 </expand>
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282 </param>
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283 <param name="entity_fill_channel" type="select" label="Entity fill channel">
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284 <expand macro="channel_options_none">
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285 <option value="all">all</option>
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286 </expand>
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287 </param>
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288 <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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289 <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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290 <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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291 <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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292 </section>
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293 <section name="task_input_data" title="Task input data" help="A list of image channels and per-channel pre-processing steps. This allows the application of intensity normalization, down-sampling, and/or blurring before performing cell segmentation.">
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294 <repeat name="task_input" min="1" max="3" title="Task input data">
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295 <param name="image_channel" type="select" optional="true" label="Image channel">
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296 <expand macro="channel_options_basic">
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297 <option value="DAPI">DAPI</option>
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298 <option value="PolyT">PolyT</option>
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299 </expand>
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300 </param>
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301 <conditional name="normalize_conditional">
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302 <param name="normalize_select" type="select" label="Perform Normalization?">
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303 <option value="Yes" selected="true">Yes</option>
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304 <option value="No">No</option>
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305 </param>
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306 <when value="Yes">
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307 <conditional name="normalize_type_conditional" label="Select normalization method">
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308 <expand macro="normalization_param"/>
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309 <when value="default"/>
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310 <when value="CLAHE">
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311 <param name="clip_limit" type="float" min="0" max="1" value="0.01" label="Clip limit" help="higher values give more contrast"/>
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312 <param name="filter_size" type="integer" min="1" value="100" label="Tile grid size"/>
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313 </when>
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314 </conditional>
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315 </when>
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316 <when value="No"/>
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317 </conditional>
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318 <conditional name="blur_conditional">
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319 <param name="blur_select" type="select" label="Perform Blur?">
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320 <option value="Yes">Yes</option>
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321 <option value="No" selected="true">No</option>
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322 </param>
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323 <when value="Yes">
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324 <param name="blur_options" type="select" label="Blur options">
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325 <option value="average">average</option>
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326 <option value="median">median</option>
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327 <option value="gaussian">gaussian</option>
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328 </param>
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329 <param name="kernel_size" type="integer" min="0" value="5" label="Kernel size in pixel"/>
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330 </when>
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331 <when value="No"/>
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332 </conditional>
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333 <conditional name="downsample_conditional">
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334 <param name="downsample_select" type="select" label="Perform downsample?">
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335 <option value="Yes">Yes</option>
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336 <option value="No" selected="true">No</option>
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337 </param>
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338 <when value="Yes">
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339 <param name="scale" type="float" min="0" value="2.0" label="Downsample" help="Reduces the size of the images during segmentation to decrease processing time" />
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340 </when>
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341 <when value="No"/>
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342 </conditional>
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343 </repeat>
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344 </section>
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345 <section name="polygon_parameters" title="Polygon parameters">
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346 <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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347 <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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348 <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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349 </section>
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350 </repeat>
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351 </section>
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352 <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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353 <param name="entity_fusion_strategy" type="select" label="Entity fusion strategy">
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354 <option value="harmonize" selected="true">harmonize (recommended)</option>
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355 <option value="union">union</option>
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356 <option value="larger">larger</option>
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357 </param>
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358 <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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359 <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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360 </section>
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361 <section name="output_files" title="Output files">
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362 <param name="entity_types_output" type="select" label="Output entity types">
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363 <option value="cell">cell</option>
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364 <option value="nucleus">nucleus</option>
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365 <option value="both">both</option>
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366 </param>
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367 </section>
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368 </section>
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369 <section name="qc_params" title="QC metrics parameters">
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370 <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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371 <sanitizer invalid_char="">
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372 <valid initial="string.letters,string.digits">
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373 <add value="_" />
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bgruening
parents:
diff changeset
374 </valid>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
375 </sanitizer>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
376 <validator type="regex">[0-9a-zA-Z_]+</validator>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
377 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
378 <param argument="--input-z-index" type="integer" min="0" value="2" label="The Z plane of the mosaic tiff images to use for the patch"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
379 <param argument="--transcript-count-filter-threshold" type="integer" min="0" value="100" label="The cell transcript count threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
380 <param argument="--volume-filter-threshold" type="integer" min="0" value="200" label="The cell volume threshold used for computing metrics and clustering"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
381 <param argument="--red-stain-name" type="select" label="The stain that will be used for red channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
382 <expand macro="channel_options_none"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
383 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
384 <param argument="--green-stain-name" type="select" label="The stain that will be used for green channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
385 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
386 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
387 <option value="DAPI">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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388 <option value="PolyT" selected="true">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
389 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
390 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
391 <param argument="--blue-stain-name" type="select" label="The stain that will be used for blue channel in images">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
392 <expand macro="channel_options_basic">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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393 <option value="None">None</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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394 <option value="DAPI" selected="true">DAPI</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
395 <option value="PolyT">PolyT</option>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
396 </expand>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
397 </param>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
398 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
399 <expand macro="advanced_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
400 </inputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
401 <outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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402 <collection name="vpt_results" type="list" label="${tool.name} on ${on_string}: VPT Results">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
403 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="csv" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
404 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
405 <collection name="vpt_boundaries" type="list" label="${tool.name} on ${on_string}: VPT segmentation boundaries">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
406 <discover_datasets pattern="(?P&lt;name&gt;.+)\.parquet$" format="parquet" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
407 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
408 <data name="vpt_qc" format="html" from_work_dir="output/metrics.html" label="${tool.name} on ${on_string}: VPT QC"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
409 <collection name="vpt_config_out" type="list" label="${tool.name} on ${on_string}: VPT Config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
410 <discover_datasets pattern="(?P&lt;name&gt;.+)\.json$" format="json" directory="output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
411 </collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
412 <expand macro="common_output"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
413 </outputs>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
414 <tests>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
415 <!-- test 1: one segmentation task -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
416 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
417 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
418 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
419 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
420 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
421 <section name="experiment_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
422 <param name="z_positions_um" value="1.5, 3, 4.5, 6, 7.5, 9, 10.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
423 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
424 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
425 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
426 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
427 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
428 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
429 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
430 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
431 <section name="channel_map">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
432 <param name="red" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
433 <param name="green" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
434 <param name="blue" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
435 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
436 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
437 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
438 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
439 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
440 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
441 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
442 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
443 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
444 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
445 <section name="task_input_data">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
446 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
447 <param name="image_channel" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
448 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
449 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
450 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
451 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
452 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
453 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
454 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
455 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
456 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
457 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
458 <param name="image_channel" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
459 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
460 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
461 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
462 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
463 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
464 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
465 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
466 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
467 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
468 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
469 <param name="image_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
470 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
471 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
472 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
473 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
474 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
475 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
476 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
477 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
478 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
479 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
480 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
481 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
482 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
483 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
484 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
485 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
486 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
487 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
488 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
489 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
490 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
491 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
492 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
493 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
494 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
495 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
496 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
497 <param name="experiment_name" value="cyto2_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
498 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
499 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
500 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
501 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
502 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
503 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
504 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
505 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
506 <has_text_matching expression="0,2,0,3,0,0,0,0,2,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
507 <has_text_matching expression="3,6,3,2,1,3,3,1,3,16,0,8,113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
508 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
509 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
510 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
511 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
512 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
513 <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
514 <has_text_matching expression=",416.540438981[0-9]+,68.7110642977[0-9]+,9.67291568732[0-9]+,64.4947481953[0-9]+,"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
515 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
516 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
517 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
518 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
519 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
520 <has_text_matching expression="86,10,285.00012,10.13364,0.0,816.0,153.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
521 <has_text_matching expression="229,10,274.95612,35.72964,0.0,723.0,390.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
522 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
523 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
524 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
525 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
526 <has_text_matching expression=",Cell count,Cell volume"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
527 <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"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
528 <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"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
529 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
530 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
531 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
532 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
533 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
534 <has_text_matching expression="813229843.0,4955524.23422[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
535 <has_text_matching expression="587668405.0,22623235.0759[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
536 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
537 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
538 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
539 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
540 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
541 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
542 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
543 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
544 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
545 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
546 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
547 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
548 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
549 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
550 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
551 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
552 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
553 <has_text text="VPT Segmentation Report (cyto2_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
554 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;814&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
555 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;654.0&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
556 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
557 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
558 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
559 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
560 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
561 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
562 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
563 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
564 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
565 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
566 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
567 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
568 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
569 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
570 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
571 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
572 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
573 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
574 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
575 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
576 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
577 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
578 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
579 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
580 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
581 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
582 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
583 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
584 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
585 <!-- test 2: two segmentation tasks -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
586 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
587 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
588 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
589 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
590 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
591 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
592 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
593 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
594 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
595 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
596 <param name="model" value="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
597 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
598 <section name="channel_map">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
599 <param name="red" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
600 <param name="green" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
601 <param name="blue" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
602 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
603 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
604 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
605 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
606 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
607 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
608 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
609 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
610 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
611 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
612 <section name="task_input_data">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
613 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
614 <param name="image_channel" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
615 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
616 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
617 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
618 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
619 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
620 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
621 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
622 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
623 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
624 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
625 <param name="image_channel" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
626 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
627 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
628 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
629 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
630 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
631 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
632 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
633 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
634 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
635 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
636 <param name="image_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
637 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
638 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
639 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
640 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
641 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
642 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
643 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
644 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
645 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
646 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
647 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
648 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
649 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
650 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
651 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
652 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
653 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
654 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
655 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
656 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
657 <param name="model" value="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
658 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
659 <section name="channel_map">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
660 <param name="blue" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
661 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
662 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
663 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
664 <param name="nuclear_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
665 <param name="entity_fill_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
666 <param name="diameter" value="55"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
667 <param name="flow_threshold" value="0.8"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
668 <param name="cellprob_threshold" value="-3.0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
669 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
670 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
671 <section name="task_input_data">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
672 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
673 <param name="image_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
674 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
675 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
676 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
677 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
678 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
679 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
680 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
681 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
682 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
683 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
684 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
685 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
686 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
687 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
688 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
689 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
690 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
691 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
692 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
693 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
694 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
695 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
696 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
697 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
698 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
699 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
700 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
701 <param name="experiment_name" value="cyto2_2task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
702 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
703 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
704 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
705 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
706 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
707 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
708 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
709 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
710 <has_text_matching expression="0,0,0,0,0,0,0,0,0,1,0,1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
711 <has_text_matching expression="1,2,0,1,2,1,3,0,3,8,0,4,18,2,1,2,2,0,0,2,1,0"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
712 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
713 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
714 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
715 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
716 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
717 <has_text_matching expression=",833.754893427[0-9]+,340.820612890[0-9]+,1.070367649097[0-9]+,334.8351650026[0-9]+,-3.129014413402[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
718 <has_text_matching expression=",879.995798798[0-9]+,357.422829969[0-9]+,2.811753148503[0-9]+,352.3315077075[0-9]+,-2.496679594480[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
719 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
720 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
721 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
722 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
723 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
724 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
725 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
726 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
727 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
728 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
729 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
730 <has_text_matching expression=",Cell count,Cell volume"/>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
731 <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"/>
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
732 <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"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
733 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
734 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
735 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
736 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
737 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
738 <has_text_matching expression="56353541.0,781480.649952[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
739 <has_text_matching expression="53118509.0,808077.377016[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
740 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
741 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
742 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
743 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
744 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
745 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
746 <has_size size="232259" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
747 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
748 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
749 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
750 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
751 <has_size size="215395" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
752 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
753 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
754 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
755 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
756 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
757 <has_text text="VPT Segmentation Report (cyto2_2task)"/>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
758 <has_text text="Cell count: &lt;b class=&quot;summary__value&quot;&gt;811&lt;/b&gt;&lt;/p&gt;"/>
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
bgruening
parents: 0
diff changeset
759 <has_text text="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;669.0&lt;/b&gt;&lt;/p&gt;"/>
0
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
760 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
761 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
762 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
763 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
764 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
765 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
766 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
767 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
768 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
769 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
770 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
771 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
772 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
773 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
774 <has_text_matching expression="cyto2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
775 <has_text_matching expression="nuclei"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
776 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
777 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
778 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
779 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
780 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
781 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
782 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
783 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
784 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
785 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
786 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
787 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
788 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
789 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
790 <!-- test 3: one segmentation task with custom weight -->
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
791 <test expect_num_outputs="5">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
792 <param name="input_images" location="https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound1_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound2_z6.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z0.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z1.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z2.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z3.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z4.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z5.tif,https://zenodo.org/records/15319018/files/mosaic_Cellbound3_z6.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z0.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z1.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z2.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z3.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z4.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z5.tif,https://zenodo.org/records/15319018/files/mosaic_DAPI_z6.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z0.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z1.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z2.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z3.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z4.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z5.tif,https://zenodo.org/records/15319018/files/mosaic_PolyT_z6.tif"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
793 <param name="input_micron_to_mosaic" location="https://zenodo.org/records/15319018/files/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
794 <param name="detected_transcripts" location="https://zenodo.org/records/15319018/files/detected_transcripts.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
795 <section name="vpt_config">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
796 <section name="segmentation_tasks">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
797 <repeat name="segmentation_task">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
798 <param name="entity_types_detected" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
799 <param name="z_layers" value="3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
800 <section name="segmentation_properties">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
801 <param name="model" value="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
802 <param name="model_dimensions" value="2D"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
803 <param name="custom_weights" location="https://zenodo.org/records/15319018/files/CP_20230830_093420"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
804 <section name="channel_map">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
805 <param name="red" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
806 <param name="green" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
807 <param name="blue" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
808 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
809 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
810 <section name="segmentation_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
811 <param name="nuclear_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
812 <param name="entity_fill_channel" value="all"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
813 <param name="diameter" value="70"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
814 <param name="flow_threshold" value="0.95"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
815 <param name="cellprob_threshold" value="-5.5"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
816 <param name="minimum_mask_size" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
817 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
818 <section name="task_input_data">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
819 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
820 <param name="image_channel" value="Cellbound1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
821 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
822 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
823 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
824 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
825 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
826 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
827 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
828 </conditional> </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
829 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
830 <param name="image_channel" value="Cellbound3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
831 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
832 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
833 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
834 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
835 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
836 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
837 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
838 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
839 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
840 <repeat name="task_input">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
841 <param name="image_channel" value="DAPI"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
842 <conditional name="normalize_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
843 <param name="normalize_select" value="Yes"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
844 <conditional name="normalize_type_conditional">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
845 <param name="normalization" value="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
846 <param name="clip_limit" value="0.01"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
847 <param name="filter_size" value="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
848 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
849 </conditional>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
850 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
851 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
852 <section name="polygon_parameters">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
853 <param name="simplification_tol" value="2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
854 <param name="smoothing_radius" value="10"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
855 <param name="minimum_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
856 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
857 </repeat>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
858 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
859 <section name="segmentation_task_fusion">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
860 <param name="entity_fusion_strategy" value="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
861 <param name="min_distance_between_entities" value="1"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
862 <param name="min_final_area" value="500"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
863 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
864 <section name="output_files">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
865 <param name="entity_types_output" value="cell"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
866 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
867 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
868 <section name="qc_params">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
869 <param name="experiment_name" value="custom_1task"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
870 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
871 <section name="advanced_output">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
872 <param name="log" value="true"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
873 </section>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
874 <output_collection name="vpt_results" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
875 <element name="cell_by_gene">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
876 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
877 <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
878 <has_text_matching expression="6,11,4,0,5,2,1,0,1,2,1,2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
879 <has_text_matching expression="0,1,0,0,0,0,1,0,0,4"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
880 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
881 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
882 <element name="cell_metadata">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
883 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
884 <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
885 <has_text_matching expression="168.0683921161[0-9]+,246.3592447472[0-9]+,-1.507707574380[0-9]+,243.9322371166[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
886 <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
887 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
888 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
889 <element name="detected_transcripts">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
890 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
891 <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
892 <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
893 <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
894 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
895 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
896 <element name="metrics">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
897 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
898 <has_text_matching expression=",Cell count,Cell volume"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
899 <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"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
900 <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"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
901 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
902 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
903 <element name="sum_signals">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
904 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
905 <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
906 <has_text_matching expression="73446567.0,1605103.666715[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
907 <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
908 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
909 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
910 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
911 <output_collection name="vpt_boundaries" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
912 <element name="cellpose2_micron_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
913 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
914 <has_size size="375308" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
915 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
916 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
917 <element name="cellpose2_mosaic_space">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
918 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
919 <has_size size="365132" delta="100"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
920 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
921 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
922 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
923 <output name="vpt_qc">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
924 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
925 <has_text text="VPT Segmentation Report (custom_1task)"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
926 <has_text_matching expression="Cell count: &lt;b class=&quot;summary__value&quot;&gt;93[0-9]+&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
927 <has_text_matching expression="Transcripts per cell - median: &lt;b class=&quot;summary__value&quot;&gt;49\d*(\.\d+)?&lt;/b&gt;&lt;/p&gt;"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
928 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
929 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
930 <output_collection name="vpt_config_out" type="list">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
931 <element name="segmentation_specification">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
932 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
933 <has_text_matching expression="input/vpt_config_file.json"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
934 <has_text_matching expression="input/images/"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
935 <has_text_matching expression="input/micron_to_mosaic_pixel_transform.csv"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
936 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
937 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
938 <element name="vpt_config_file">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
939 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
940 <has_text_matching expression="0,1,2,3,4,5,6"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
941 <has_text_matching expression="Cellpose2"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
942 <has_text_matching expression="null"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
943 <has_text_matching expression="CLAHE"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
944 <has_text_matching expression="harmonize"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
945 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
946 </element>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
947 </output_collection>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
948 <output name="vpt_log">
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
949 <assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
950 <has_text_matching expression="run_segmentation finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
951 <has_text_matching expression="Partition transcripts finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
952 <has_text_matching expression="Sum signals finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
953 <has_text_matching expression="Generate segmentation metrics finished"/>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
954 </assert_contents>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
955 </output>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
956 </test>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
957 </tests>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
958 <help>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
959 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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
960
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
961 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
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
962
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
963 Segmentation parameters for CellPose can be assigned with "**Segmentation configuration file**".
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
964
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
965 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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
966
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
967 The segmentation parameters has 3 main sections:
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
968
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
969 1. **Experiment properties**:
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
970 - 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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
971 2. **Segmentation tasks**:
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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972 - 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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
973 3. **Segmentation task fusion**:
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
974 - 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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
975 4. **Output files**:
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
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diff changeset
976 - Specifies which entity types should be written to disk in the output folder and the file names they should receive.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
977
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
978
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
979 For more information on the VPT pipeline, please refer to the `VPT user guide`_
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
980
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
981 -----
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
982
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
983 If you want to use a custom-trained model, set the CellPose model to null and provide the custom weights file.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
984
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
985
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
986 .. class:: infomark
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
987
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
988 **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.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
989
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
990 .. class:: infomark
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
991
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
992 **Note:** VPT tool on Galaxy only uses **CellPose** algorithm for cell segmentation.
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
993
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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parents:
diff changeset
994 .. _`VPT user guide`: https://vizgen.github.io/vizgen-postprocessing/
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
995 </help>
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
bgruening
parents:
diff changeset
996 <expand macro="citations" />
5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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diff changeset
997 </tool>