Mercurial > repos > ebi-gxa > scanpy_compute_graph

comparison scanpy-neighbours.xml @ 12:c78c930e3263 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 14:02:36 +0000
parents 232937b5bb8f
children e6c989a9211c
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11:232937b5bb8f 12:c78c930e3263
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>