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comparison gate_finder.xml @ 0:6df8d6e42152 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/vitessce commit 9b2dc921e692af8045773013d9f87d4d790e2ea1
author goeckslab
date Thu, 08 Sep 2022 17:22:53 +0000
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1 <tool id="gate_finder" name="Gate Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>displays a series of gating outcomes using Vitessce</description>
3 <macros>
4 <import>main_macros.xml</import>
5 </macros>
6 <expand macro="vitessce_requirements"/>
7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command>
9 <expand macro="vitessce_cmd" tool_id="gate_finder" />
10 <configfiles>
11 <inputs name="inputs" />
12 </configfiles>
13 <inputs>
14 <param name="image" type="data" format="ome.tiff" label="Select the image (OME-TIFF)" />
15 <param name="masks" type="data" format="tiff,ome.tiff" optional="true" label="Select masks for the OME Tiff image (Optional)" />
16 <section name="do_phenotyping" title=" ">
17 <param name="phenotyping_choice" type="hidden" value="true"/>
18 </section>
19 <param name="phenotyping_choice" type="hidden" value="yes" />
20 <param name="anndata" type="data" format="h5ad" label="Select the anndata containing marker intensities" />
21 <param name="marker" type="text" value="" label="Marker for which gate is to be defined" help="E.g.: CD45." />
22 <param name="from_gate" type="integer" value="6" label="Start value gate of interest" help="Integer. Optional" />
23 <param name="to_gate" type="integer" value="8" label="End value of the gate of interest." help="Integer. Optional" />
24 <param name="increment" type="float" value="0.1" label="Increments between the start and end values" help="Float." />
25 <param name="x_coordinate" type="text" value="X_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
26 <param name="y_coordinate" type="text" value="Y_centroid" optional="true" label="X axis coordinate column name in AnnData object" />
27 </inputs>
28 <outputs>
29 <data format="html" name="output" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="image" value="cropped_reactive_core.ome.tiff" ftype="ome.tiff" />
34 <param name="anndata" value="cropped_tutorial_data_pheno.h5ad" ftype="h5ad" />
35 <param name="marker" value="CD45" />
36 <param name="from_gate" value="5" />
37 <param name="to_gate" value="9" />
38 <param name="increment" value="0.5" />
39 <output name="output" file="tutorial_vitessce.html" compare="sim_size" delta="20" />
40 </test>
41 </tests>
42 <help>
43 <![CDATA[
44 **What it does**
45 This tool, built on top of vitessce visualization components, mimics the find_gate function from scimap (https://scimap.xyz/) to do manual gating for single cell quantification data.
46
47 **Input**
48
49 OME-TIFF image.
50 Segmentation masks (optional).
51 AnnData with marker intensities.
52
53 **Output**
54
55 An HTML file with Vitessce component.
56
57
58 ]]>
59 </help>
60 <citations>
61 <citation type="doi">10.31219/osf.io/y8thv</citation>
62 </citations>
63 </tool>