Mercurial > repos > goeckslab > scimap_spatial

comparison scimap_spatial.xml @ 2:d19c068c2490 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 18:44:35 +0000
parents 42e6c251bfd0
children 472780baf150
comparison
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1:fd38e533a54b 2:d19c068c2490
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 '$__tool_directory__/scimap_spatial.py' 12 python '$__tool_directory__/scimap_spatial.py'
13 --inputs '$inputs' 13 --inputs '$inputs'
14 --anndata '$anndata' 14 --anndata '$anndata'
15 --output '$output' 15 --output '$output'
35 <when value="cluster"> 35 <when value="cluster">
36 <param name="method" type="select" label="Select the clustering method"> 36 <param name="method" type="select" label="Select the clustering method">
37 <option value="kmeans" selected="true">kmeans</option> 37 <option value="kmeans" selected="true">kmeans</option>
38 <option value="phenograph">phenograph</option> 38 <option value="phenograph">phenograph</option>
39 <option value="leiden">leiden</option> 39 <option value="leiden">leiden</option>
40 <option value="parc">parc</option>
41 </param> 40 </param>
42 <section name="options" title="Advanced Options" expanded="false"> 41 <section name="options" title="Advanced Options" expanded="false">
43 <param argument="subset_genes" type="text" value="" optional="true" label="Type in a list of genes that should be included for the purpose of clustering" help="Optional. Comma delimited. By default the algorithm uses all genes in the dataset." /> 42 <param argument="subset_genes" type="text" value="" optional="true" label="Type in a list of genes that should be included for the purpose of clustering" help="Optional. Comma delimited. By default the algorithm uses all genes in the dataset." />
44 <param argument="sub_cluster" type="boolean" checked="false" optional="true" label="Whether to do sub-clustering on existing clustering or phenotyping " /> 43 <param argument="sub_cluster" type="boolean" checked="false" optional="true" label="Whether to do sub-clustering on existing clustering or phenotyping " />
45 <param argument="sub_cluster_column" type="text" value="phenotype" optional="true" label="Type in the name of a column to be sub-clustered" help="This is only required when sub_cluster is set to True." /> 44 <param argument="sub_cluster_column" type="text" value="phenotype" optional="true" label="Type in the name of a column to be sub-clustered" help="This is only required when sub_cluster is set to True." />
46 <param argument="sub_cluster_group" type="text" value="" optional="true" label="Type in a list of group names within the sub-cluster column" help="Optional. Comma delimited. By default the program will sub-cluster all groups within column passed through the argument sub_cluster_column." /> 45 <param argument="sub_cluster_group" type="text" value="" optional="true" label="Type in a list of group names within the sub-cluster column" help="Optional. Comma delimited. By default the program will sub-cluster all groups within column passed through the argument sub_cluster_column." />
47 <param argument="parc_small_pop" type="integer" value="50" optional="true" label="Smallest cluster population to be considered a community in PARC clustering" />
48 <param argument="parc_too_big_factor" type="float" value="0.4" optional="true" label="If a cluster exceeds this share of the entire cell population, then the PARC will be run on the large cluster" />
49 <param argument="k" type="integer" value="10" optional="true" label="Number of clusters to return when using K-Means clustering" /> 46 <param argument="k" type="integer" value="10" optional="true" label="Number of clusters to return when using K-Means clustering" />
50 <param argument="n_pcs" type="integer" value="" optional="true" label="Number of PC's to be used in leiden clustering" help="By default it uses all PC's" /> 47 <param argument="n_pcs" type="integer" value="" optional="true" label="Number of PC's to be used in leiden clustering" help="By default it uses all PC's" />
51 <param argument="resolution" type="float" value="1" optional="true" label="A parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters." /> 48 <param argument="resolution" type="float" value="1" optional="true" label="A parameter value controlling the coarseness of the clustering" help="Higher values lead to more clusters." />
52 <param argument="phenograph_clustering_metric" type="select" label="Distance metric to define nearest neighbors"> 49 <param argument="phenograph_clustering_metric" type="select" label="Distance metric to define nearest neighbors">
53 <option value="euclidean" selected="true">euclidean</option> 50 <option value="euclidean" selected="true">euclidean</option>
167 <outputs> 164 <outputs>
168 <data format="h5ad" name="output" label="Scimap.tools.${analyses.selected_tool} on ${on_string}" /> 165 <data format="h5ad" name="output" label="Scimap.tools.${analyses.selected_tool} on ${on_string}" />
169 </outputs> 166 </outputs>
170 <tests> 167 <tests>
171 <test> 168 <test>
172 <param name="anndata" value="imc.h5ad" /> 169 <param name="anndata" value="tutorial_data_pheno.h5ad" />
173 <conditional name="analyses"> 170 <conditional name="analyses">
174 <param name="selected_tool" value="cluster" /> 171 <param name="selected_tool" value="cluster" />
175 <param name="method" value="kmeans" /> 172 <param name="method" value="kmeans" />
176 </conditional> 173 </conditional>
177 <output name="output"> 174 <output name="output">
207 Anndata with a corresponding key added. 204 Anndata with a corresponding key added.
208 205
209 206
210 ]]> 207 ]]>
211 </help> 208 </help>
212 <citations> 209 <expand macro="citations" />
213 </citations>
214 </tool> 210 </tool>