Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 23:bc9e8de21efb draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"
author ebi-gxa
date Fri, 23 Jul 2021 08:28:48 +0000
parents a30d21fd5319
children fcaa9048cdaf
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22:a30d21fd5319 23:bc9e8de21efb
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive kNN graph</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
29 #end if 29 #end if
30 30
31 --method '${settings.method}' 31 --method '${settings.method}'
32 --metric '${settings.metric}' 32 --metric '${settings.metric}'
33 --random-state '${settings.random_seed}' 33 --random-state '${settings.random_seed}'
34 #if $settings.use_rep != "auto" 34 #if $settings.use_rep
35 --use-rep '${settings.use_rep}' 35 --use-rep '${settings.use_rep}'
36 #end if 36 #end if
37 #if $settings.n_pcs 37 #if $settings.n_pcs
38 --n-pcs '${settings.n_pcs}' 38 --n-pcs '${settings.n_pcs}'
39 #end if 39 #end if
53 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added" 53 <param name="key_added" argument="--key-added" type="text" optional="true" label="Key added"
54 help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='' /> 54 help="If not specified, the neighbors data is stored in .uns[‘neighbors’], distances and connectivities are stored in .obsp[‘distances’] and .obsp[‘connectivities’] respectively. If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added+’_distances’] and connectivities in .obsp[key_added+’_connectivities’]." value='' />
55 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> 55 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/>
56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" 56 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true"
57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> 57 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/>
58 <param name="use_rep" type="select" label="Use the indicated representation"> 58 <param name="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="'X' (for the content of .X, usually normalised expression values) or any key for .obsm (e.g. X_pca for PCA) is valid. If not set, the representation is chosen automatically: For .n_vars less than 50, .X is used, otherwise ‘X_pca’ is used. If ‘X_pca’ is not present, it’s computed with default parameters."/>
59 <option value="X_pca" selected="true">X_pca, use PCs</option>
60 <option value="X">X, use normalised expression values</option>
61 <option value="X_diffmap"> X_diffmap, use diffusion map</option>
62 </param>
63 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> 59 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/>
64 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" 60 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true"
65 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> 61 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/>
66 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> 62 <param name="method" argument="--method" type="select" label="Method for calculating connectivity">
67 <option value="umap" selected="true">UMAP</option> 63 <option value="umap" selected="true">UMAP</option>