Mercurial > repos > goeckslab > gate_finder

comparison gate_finder.xml @ 4:5f4a4dd06bc9 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 19:47:28 +0000
parents 8097f9124f87
children
comparison
equal deleted inserted replaced
3:80102785f5ff 4:5f4a4dd06bc9
6 <edam_operations> 6 <edam_operations>
7 <edam_operation>operation_3443</edam_operation> 7 <edam_operation>operation_3443</edam_operation>
8 </edam_operations> 8 </edam_operations>
9 <expand macro="vitessce_requirements"/> 9 <expand macro="vitessce_requirements"/>
10 <expand macro="macro_stdio" /> 10 <expand macro="macro_stdio" />
11 <version_command>echo "@VERSION@"</version_command> 11 <version_command>echo "@TOOL_VERSION@"</version_command>
12 <expand macro="vitessce_cmd" tool_id="gate_finder" /> 12 <expand macro="vitessce_cmd" tool_id="gate_finder" />
13 <configfiles> 13 <configfiles>
14 <inputs name="inputs" /> 14 <inputs name="inputs" />
15 </configfiles> 15 </configfiles>
16 <inputs> 16 <inputs>
28 <param name="x_coordinate" type="text" value="X_centroid" optional="true" label="X axis coordinate column name in AnnData object" /> 28 <param name="x_coordinate" type="text" value="X_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
29 <param name="y_coordinate" type="text" value="Y_centroid" optional="true" label="X axis coordinate column name in AnnData object" /> 29 <param name="y_coordinate" type="text" value="Y_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data format="html" name="output" /> 32 <data format="html" name="output" />
33 <data format="json" name="vitessce_config" from_work_dir="config.json" hidden="true" label="Vitessce config file on ${on_string}" />
33 </outputs> 34 </outputs>
34 <tests> 35 <tests>
35 <test> 36 <test>
36 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" /> 37 <param name="image" value="vitessce_image.ome.tiff" ftype="ome.tiff" />
37 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" /> 38 <param name="masks" value="vitessce_mask.tiff" ftype="tiff" />
38 <param name="marker" value="CD45" /> 39 <param name="anndata" value="vitessce_test.h5ad" ftype="h5ad" />
39 <param name="from_gate" value="5" /> 40 <param name="marker" value="DNA_1" />
40 <param name="to_gate" value="9" /> 41 <param name="from_gate" value="6" />
41 <param name="increment" value="0.5" /> 42 <param name="to_gate" value="8" />
42 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" /> 43 <param name="increment" value=".1" />
44 <output name="vitessce_config">
45 <assert_contents>
46 <has_json_property_with_text property="name" text="OMETIFF" />
47 <has_json_property_with_text property="name" text="MASKS" />
48 <has_json_property_with_text property="name" text="DNA_1--6.0" />
49 <has_json_property_with_text property="name" text="DNA_1--7.9" />
50 </assert_contents>
51 </output>
43 </test> 52 </test>
44 </tests> 53 </tests>
45 <help> 54 <help>
46 <![CDATA[ 55 <![CDATA[
47 **What it does** 56 **What it does**