Mercurial > repos > goeckslab > vitessce_spatial

comparison vitessce_spatial.xml @ 4:068da7f7cd83 draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit bc4c0bb6784a55399241f99a29b176541a164a18
author goeckslab
date Thu, 20 Feb 2025 19:47:16 +0000
parents 4bf852448b5d
children
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3:7cc457aa78b1 4:068da7f7cd83
1 <tool id="vitessce_spatial" name="Run multi-modal single-cell visualization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="vitessce_spatial" name="Vitessce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>with Vitessce</description> 2 <description>Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments</description>
3 3
4 <macros> 4 <macros>
5 <import>main_macros.xml</import> 5 <import>main_macros.xml</import>
6 </macros> 6 </macros>
7 7
9 <edam_operation>operation_3443</edam_operation> 9 <edam_operation>operation_3443</edam_operation>
10 </edam_operations> 10 </edam_operations>
11 11
12 <expand macro="vitessce_requirements"/> 12 <expand macro="vitessce_requirements"/>
13 <expand macro="macro_stdio" /> 13 <expand macro="macro_stdio" />
14 <version_command> "@VERSION@"</version_command> 14 <version_command>echo "@TOOL_VERSION@"</version_command>
15 <expand macro="vitessce_cmd" /> 15 <expand macro="vitessce_cmd" />
16 16
17 <configfiles> 17 <configfiles>
18 <inputs name="inputs" /> 18 <inputs name="inputs" />
19 </configfiles> 19 </configfiles>
86 </when> 86 </when>
87 </conditional> 87 </conditional>
88 </inputs> 88 </inputs>
89 <outputs> 89 <outputs>
90 <data format="html" name="output" /> 90 <data format="html" name="output" />
91 <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" />
91 </outputs> 92 </outputs>
92 <tests> 93 <tests>
93 <test> 94 <test>
94 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> 95 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
95 <conditional name="do_phenotyping"> 96 <conditional name="do_phenotyping">
96 <param name="phenotyping_choice" value="add_h5ad" /> 97 <param name="phenotyping_choice" value="add_h5ad" />
97 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> 98 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
98 <conditional name="phenotype_factory">
99 <param name="phenotype_mode" value="type_in" />
100 <param name="phenotypes" value="leiden" />
101 </conditional>
102 </conditional> 99 </conditional>
103 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> 100 <output name="vitessce_config">
101 <assert_contents>
102 <has_json_property_with_text property="name" text="OMETIFF" />
103 <has_json_property_with_text property="path" text="obs/phenotype" />
104 </assert_contents>
105 </output>
104 </test> 106 </test>
105 <test> 107 <test>
106 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> 108 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
109 <param name="masks" value="vitessce_mask.tiff" ftype="tiff" />
107 <conditional name="do_phenotyping"> 110 <conditional name="do_phenotyping">
108 <param name="phenotyping_choice" value="add_h5ad" /> 111 <param name="phenotyping_choice" value="add_h5ad" />
109 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> 112 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
110 <conditional name="scatterplot_embeddings">
111 <param name="embedding" value="pca" />
112 </conditional>
113 <conditional name="phenotype_factory">
114 <param name="phenotype_mode" value="type_in" />
115 <param name="phenotypes" value="leiden" />
116 </conditional>
117 </conditional> 113 </conditional>
118 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> 114 <output name="vitessce_config">
119 </test> 115 <assert_contents>
120 <test> 116 <has_json_property_with_text property="name" text="OMETIFF" />
121 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> 117 <has_json_property_with_text property="name" text="MASKS" />
122 <conditional name="do_phenotyping"> 118 <has_json_property_with_text property="path" text="obs/phenotype" />
123 <param name="phenotyping_choice" value="no_h5ad" /> 119 </assert_contents>
124 </conditional> 120 </output>
125 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />
126 </test> 121 </test>
127 </tests> 122 </tests>
128 <help> 123 <help>
129 <![CDATA[ 124 <![CDATA[
130 **What it does** 125 **What it does**