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comparison scimap_phenotyping.xml @ 0:7ed4b55b11f7 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit b19cb55dfb751cccc857b95a432890299bfeebb5
author goeckslab
date Tue, 19 Jul 2022 20:29:22 +0000
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1 <tool id="scimap_phenotyping" name="Single Cell Phenotyping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>using scimap</description>
3 <macros>
4 <import>main_macros.xml</import>
5 </macros>
6
7 <expand macro="scimap_requirements"/>
8 <expand macro="macro_stdio" />
9 <version_command>echo "@VERSION@"</version_command>
10 <command>
11 <![CDATA[
12 python '$__tool_directory__/scimap_phenotyping.py'
13 --adata '$anndata'
14 #if $manual_gates
15 --manual_gates '$manual_gates'
16 --manual_gates_ext '${manual_gates.ext}'
17 #end if
18 --gating_workflow '$gating_workflow'
19 --gating_workflow_ext '${gating_workflow.ext}'
20 #if $rescale_plots
21 --rescale_plots
22 #end if
23 --output '$output'
24
25 ]]>
26 </command>
27 <configfiles>
28 <inputs name="inputs" />
29 </configfiles>
30 <inputs>
31 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
32 <param name="manual_gates" type="data" format="tabular,csv" optional="true" label="Select the dataset containing manual gate information" help="First column as markers and second column as the gate values in log1p scale. If a marker is not included, auto gating
33 based on gaussian mixture modeling will be executed. Optional."/>
34 <param name="gating_workflow" type="data" format="tabular,csv" label="Select the dataset containing gating workflow" />
35 <param name="rescale_plots" type="boolean" checked="false" label="Save the GMM gates plots If True"/>
36 </inputs>
37 <outputs>
38 <data format="h5ad" name="output" />
39 <collection name="gmm_plots" type="list" label="${tool.name}: GMM-plots">
40 <filter>rescale_plots</filter>
41 <discover_datasets pattern="__designation_and_ext__" directory="auto_gating" ext="png"/>
42 </collection>
43 </outputs>
44 <tests>
45 <test>
46 <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" />
47 <param name="manual_gates" value="manual_gates.csv" ftype="csv" />
48 <param name="gating_workflow" value="phenotype_workflow.csv" ftype="csv" />
49 <output name="output">
50 <assert_contents>
51 <has_h5_keys keys="obs/phenotype" />
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help>
57 <![CDATA[
58 **What it does**
59
60 This tool generates single cell phenotyping using either manual gating or auto gating (gaussian mixture modeling) implemented in Scimap.
61
62 **Input**
63
64 AnnData.
65
66 **Output**
67
68 Anndata with "obs/phenotype" added.
69
70
71 ]]>
72 </help>
73 <citations>
74 </citations>
75 </tool>