Mercurial > repos > goeckslab > vitessce_spatial

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit a3dd8a6f384e5227972910c80d280250e28d1432
author goeckslab
date Fri, 06 Jun 2025 16:38:33 +0000
parents 97be83fc3677
children
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1 <tool id="vitessce_spatial" name="Vitessce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments</description>
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4 <macros>
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5 <import>main_macros.xml</import>
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6 </macros>
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8 <edam_operations>
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9 <edam_operation>operation_3443</edam_operation>
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10 </edam_operations>
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11
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12 <expand macro="vitessce_requirements"/>
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13 <expand macro="macro_stdio" />
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14 <version_command>echo "@TOOL_VERSION@"</version_command>
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15 <expand macro="vitessce_cmd" />
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17 <configfiles>
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18 <inputs name="inputs" />
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19 <configfile name="galaxy_config">
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20 <![CDATA[
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21 {
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22 "galaxy_url": "${__app__.config.galaxy_infrastructure_url}",
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23 "dataset_id": "${__app__.security.encode_id($output.id)}"
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24 }
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25 ]]>
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26 </configfile>
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27 </configfiles>
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28
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29 <inputs>
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30 <param name="image" type="data" format="ome.tiff" label="Select the OME Tiff image" />
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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31 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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32 <conditional name="do_phenotyping">
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33 <param name="phenotyping_choice" type="select" label="Add annotations or visualizations from Anndata file">
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34 <option value="no_h5ad" selected="true">Do not add elements from Anndata file</option>
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35 <option value="add_h5ad">Add elements from Anndata file</option>
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36 </param>
1
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37 <when value="no_h5ad">
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38 </when>
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39 <when value="add_h5ad">
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40 <param name="anndata" type="data" format="h5ad" label="Select the anndata file" />
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41 <conditional name="scatterplot_embeddings">
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42 <param name="embedding" type="select" label="Select an embedding algorithm for scatterplot">
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43 <option value="umap" selected="true">UMAP</option>
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44 <option value="tsne">tSNE</option>
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45 <option value="pca">PCA</option>
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46 </param>
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47 <when value="umap">
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48 <section name="options" title="Advance Options for neighbor search">
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49 <param argument="n_neighbors" type="integer" value="30" label="The size of local neighborhood used for manifold approximation" />
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50 <param argument="n_pcs" type="integer" value="10" label="Number of PCs" />
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51 <param argument="knn" type="boolean" checked="true" label="Whether to use knn graph" help="If false, use a Gaussian Kernel to assign low weights to neighbors more distant than the n_neighbors nearest neighbor." />
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52 <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" />
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53 </section>
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54 </when>
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55 <when value="tsne">
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56 <section name="options" title="Advance Options for computing tSNE">
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57 <param argument="n_pcs" type="integer" value="10" label="Number of PCs" />
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58 <param argument="learning_rate" type="float" value="1000" label="Learning rate" help="Should be 100-1000." />
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59 <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" />
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60 </section>
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61 </when>
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62 <when value="pca">
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63 <section name="options" title="Advance Options for computing PCA">
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64 <param argument="n_comps" type="integer" value="" optional="true" label="Number of principal components to compute" help="Defaults to 50, or 1 - minimum dimension size of selected representation." />
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65 <param argument="zero_center" type="boolean" checked="true" label="Whether to compute standard PCA from covariance matrix" help="If False, omit zero-centering variables (uses TruncatedSVD)" />
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66 <param argument="svd_solver" type="select" label="Select the SVD solver">
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67 <option value="arpack" selected="true">arpack</option>
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68 <option value="randomized">randomized</option>
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69 <option value="auto">auto</option>
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70 <option value="lobpcg">lobpcg</option>
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71 </param>
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72 <param argument="random_state" type="integer" value="0" optional="true" label="Randomness seed" />
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73 </section>
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74 </when>
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75 </conditional>
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76 <conditional name="phenotype_factory">
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77 <param name="phenotype_mode" type="select" label="Input the anndata key to display">
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78 <option value="choices" selected="true">Multiple choices</option>
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79 <option value="type_in">Type in</option>
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80 </param>
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81 <when value="choices">
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82 <param name="phenotypes" type="select" multiple="true" display="checkboxes" label="Select the key(s)" >
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83 <option value="phenotype" selected="true">'phenotype' (via scimap phenotyping)</option>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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84 <option value="kmeans">'kmeans' (via clustering)</option>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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85 <option value="leiden">'leiden' (via clustering)</option>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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86 <option value="phenograph">'phenograph' (via clustering)</option>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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87 <option value="parc">'parc' (via clustering)</option>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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88 </param>
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89 </when>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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90 <when value="type_in">
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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91 <param name="phenotypes" type="text" value="" label="Type in the keys storing phenotypes" help="Comma delimited for multiple keys."/>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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92 </when>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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93 </conditional>
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94 </when>
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95 </conditional>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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96 </inputs>
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97 <outputs>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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98 <data format="html" name="output" />
5
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99 <data format="json"
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100 name="vitessce_config"
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101 from_work_dir="config.json"
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102 hidden="true"
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103 label="Vitessce config file on ${on_string}">
97be83fc3677 planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 90f081e58b5ee41bba3a7e6f01d97b5bd9392759
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104 </data>
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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105 </outputs>
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106 <tests>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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107 <test>
4
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108 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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109 <conditional name="do_phenotyping">
1
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110 <param name="phenotyping_choice" value="add_h5ad" />
4
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111 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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112 </conditional>
4
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113 <output name="vitessce_config">
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114 <assert_contents>
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115 <has_json_property_with_text property="name" text="OMETIFF" />
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116 <has_json_property_with_text property="path" text="obs/phenotype" />
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117 </assert_contents>
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118 </output>
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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119 </test>
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120 <test>
4
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121 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
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122 <param name="masks" value="vitessce_mask.tiff" ftype="tiff" />
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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123 <conditional name="do_phenotyping">
4
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124 <param name="phenotyping_choice" value="add_h5ad" />
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125 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
0
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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126 </conditional>
4
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127 <output name="vitessce_config">
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128 <assert_contents>
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129 <has_json_property_with_text property="name" text="OMETIFF" />
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130 <has_json_property_with_text property="name" text="MASKS" />
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131 <has_json_property_with_text property="path" text="obs/phenotype" />
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132 </assert_contents>
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133 </output>
0
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134 </test>
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135 </tests>
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136 <help>
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137 <![CDATA[
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138 **What it does**
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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139 This tools provides web-based, interactive and scalable visualizations of single cell data.
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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140
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141 **Input**
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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142
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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143 OME-TIFF image.
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144 Segmentation masks (optional).
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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145 AnnData with marker intensities.
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146
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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147 **Output**
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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148
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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149 An HTML file with Vitessce component.
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150
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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151 ]]>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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152 </help>
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153 <citations>
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154 <citation type="doi">10.31219/osf.io/y8thv</citation>
9f60ef2d586e planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
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155 </citations>
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156 </tool>