Mercurial > repos > ebi-gxa > scanpy_compute_graph
comparison scanpy-neighbours.xml @ 12:c78c930e3263 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author | ebi-gxa |
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date | Mon, 07 Sep 2020 14:02:36 +0000 |
parents | 232937b5bb8f |
children | e6c989a9211c |
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11:232937b5bb8f | 12:c78c930e3263 |
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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@+galaxy11" profile="@PROFILE@"> | 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" 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"/> |
13 --n-neighbors \$( cat $settings.n_neighbors_file ) | 13 --n-neighbors \$( cat $settings.n_neighbors_file ) |
14 #elif $settings.n_neighbors | 14 #elif $settings.n_neighbors |
15 --n-neighbors '${settings.n_neighbors}' | 15 --n-neighbors '${settings.n_neighbors}' |
16 #end if | 16 #end if |
17 --method '${settings.method}' | 17 --method '${settings.method}' |
18 --metric '${settings.metric}' | |
18 --random-state '${settings.random_seed}' | 19 --random-state '${settings.random_seed}' |
19 #if $settings.use_rep != "auto" | 20 #if $settings.use_rep != "auto" |
20 --use-rep '${settings.use_rep}' | 21 --use-rep '${settings.use_rep}' |
21 #end if | 22 #end if |
22 #if $settings.n_pcs | 23 #if $settings.n_pcs |
36 <when value="true"/> | 37 <when value="true"/> |
37 <when value="false"> | 38 <when value="false"> |
38 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> | 39 <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> |
39 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" | 40 <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" |
40 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> | 41 label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> |
41 <param name="use_rep" type="text" label="Use the indicated representation"> | 42 <param name="use_rep" type="select" label="Use the indicated representation"> |
42 <option value="X_pca" selected="true">X_pca, use PCs</option> | 43 <option value="X_pca" selected="true">X_pca, use PCs</option> |
43 <option value="X">X, use normalised expression values</option> | 44 <option value="X">X, use normalised expression values</option> |
44 </param> | 45 </param> |
45 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> | 46 <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> |
46 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" | 47 <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" |
47 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> | 48 label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> |
48 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> | 49 <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> |
49 <option value="umap" selected="true">UMAP</option> | 50 <option value="umap" selected="true">UMAP</option> |
50 <option value="gauss">Gaussian</option> | 51 <option value="gauss">Gaussian</option> |
52 <option value="rapids">RAPIDS</option> | |
53 </param> | |
54 <param name="metric" argument="--metric" type="select" label="A known metric’s name"> | |
55 <option value="euclidean" selected="true">Euclidean</option> | |
56 <option value="cityblock">cityblock</option> | |
57 <option value="cosine">cosine</option> | |
58 <option value="l1">l1</option> | |
59 <option value="l2">l2</option> | |
60 <option value="manhattan">manhattan</option> | |
61 <option value="braycurtis">braycurtis</option> | |
62 <option value="canberra">canberra</option> | |
63 <option value="chebyshev">chebyshev</option> | |
64 <option value="correlation">correlation</option> | |
65 <option value="dice">dice</option> | |
66 <option value="hamming">hamming</option> | |
67 <option value="jaccard">jaccard</option> | |
68 <option value="kulsinski">kulsinski</option> | |
69 <option value="mahalanobis">mahalanobis</option> | |
70 <option value="minkowski">minkowski</option> | |
71 <option value="rogerstanimoto">rogerstanimoto</option> | |
72 <option value="russelrao">russelrao</option> | |
73 <option value="seuclidan">seuclidian</option> | |
74 <option value="sokalmichener">sokalmichener</option> | |
75 <option value="sokalsneath">sokalsneath</option> | |
76 <option value="sqeuclidean">sqeuclidean</option> | |
77 <option value="yule">yule</option> | |
51 </param> | 78 </param> |
52 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> | 79 <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> |
53 </when> | 80 </when> |
54 </conditional> | 81 </conditional> |
55 </inputs> | 82 </inputs> |