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comparison scimap_phenotyping.xml @ 2:ce22e846c5e4 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:44:25 +0000
parents 7ed4b55b11f7
children
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1:dcfcad35e847 2:ce22e846c5e4
5 </macros> 5 </macros>
6 6
7 <expand macro="scimap_requirements"/> 7 <expand macro="scimap_requirements"/>
8 <expand macro="macro_stdio" /> 8 <expand macro="macro_stdio" />
9 <version_command>echo "@VERSION@"</version_command> 9 <version_command>echo "@VERSION@"</version_command>
10 <command> 10 <command detect_errors="aggressive">
11 <![CDATA[ 11 <![CDATA[
12 python '$__tool_directory__/scimap_phenotyping.py' 12 python '$__tool_directory__/scimap_phenotyping.py'
13 --adata '$anndata' 13 --adata '$anndata'
14 #if $log
15 --log
16 #end if
14 #if $manual_gates 17 #if $manual_gates
15 --manual_gates '$manual_gates' 18 --manual_gates '$manual_gates'
16 --manual_gates_ext '${manual_gates.ext}' 19 --manual_gates_ext '${manual_gates.ext}'
17 #end if 20 #end if
18 --gating_workflow '$gating_workflow' 21 --gating_workflow '$gating_workflow'
19 --gating_workflow_ext '${gating_workflow.ext}' 22 --gating_workflow_ext '${gating_workflow.ext}'
20 #if $rescale_plots 23 --random_state '$random_state'
21 --rescale_plots
22 #end if
23 --output '$output' 24 --output '$output'
24 25
25 ]]> 26 ]]>
26 </command> 27 </command>
27 <configfiles> 28 <configfiles>
28 <inputs name="inputs" /> 29 <inputs name="inputs" />
29 </configfiles> 30 </configfiles>
30 <inputs> 31 <inputs>
31 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" /> 32 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
33 <param name="log" type="boolean" checked="true" label="Whether to log the data prior to rescaling" />
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 34 <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."/> 35 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" /> 36 <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"/> 37 <param name="random_state" type="integer" value="0" optional="true" label="Set seed used by the random number generator for GMM" />
36 </inputs> 38 </inputs>
37 <outputs> 39 <outputs>
38 <data format="h5ad" name="output" /> 40 <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> 41 </outputs>
44 <tests> 42 <tests>
45 <test> 43 <test>
46 <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" /> 44 <param name="anndata" value="tutorial_data.h5ad" ftype="h5ad" />
47 <param name="manual_gates" value="manual_gates.csv" ftype="csv" /> 45 <param name="manual_gates" value="manual_gates.csv" ftype="csv" />
61 59
62 **Input** 60 **Input**
63 61
64 AnnData. 62 AnnData.
65 63
64 **Important Note**
65
66 If adata.raw.X exists, it will be used. If adata.raw.X does not exist, adata.X is used
67
66 **Output** 68 **Output**
67 69
68 Anndata with "obs/phenotype" added. 70 Anndata with "obs/phenotype" added.
69 71
70 72
71 ]]> 73 ]]>
72 </help> 74 </help>
73 <citations> 75 <expand macro="citations" />
74 </citations>
75 </tool> 76 </tool>