Mercurial > repos > ebi-gxa > scanpy_compute_graph
diff 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 |
---|---|
date | Mon, 07 Sep 2020 14:02:36 +0000 |
parents | 232937b5bb8f |
children | e6c989a9211c |
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--- a/scanpy-neighbours.xml Fri Jun 05 09:12:59 2020 -0400 +++ b/scanpy-neighbours.xml Mon Sep 07 14:02:36 2020 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy11" profile="@PROFILE@"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> @@ -15,6 +15,7 @@ --n-neighbors '${settings.n_neighbors}' #end if --method '${settings.method}' + --metric '${settings.metric}' --random-state '${settings.random_seed}' #if $settings.use_rep != "auto" --use-rep '${settings.use_rep}' @@ -38,7 +39,7 @@ <param name="n_neighbors" argument="--n-neighbors" type="integer" value="15" label="Maximum number of neighbors used"/> <param name="n_neighbors_file" argument="--n-neighbors" type="data" format="txt,tsv" optional="true" label="File with n_neighbours, use with parameter iterator. Overrides the n_neighbors setting"/> - <param name="use_rep" type="text" label="Use the indicated representation"> + <param name="use_rep" type="select" label="Use the indicated representation"> <option value="X_pca" selected="true">X_pca, use PCs</option> <option value="X">X, use normalised expression values</option> </param> @@ -48,6 +49,32 @@ <param name="method" argument="--method" type="select" label="Method for calculating connectivity"> <option value="umap" selected="true">UMAP</option> <option value="gauss">Gaussian</option> + <option value="rapids">RAPIDS</option> + </param> + <param name="metric" argument="--metric" type="select" label="A known metric’s name"> + <option value="euclidean" selected="true">Euclidean</option> + <option value="cityblock">cityblock</option> + <option value="cosine">cosine</option> + <option value="l1">l1</option> + <option value="l2">l2</option> + <option value="manhattan">manhattan</option> + <option value="braycurtis">braycurtis</option> + <option value="canberra">canberra</option> + <option value="chebyshev">chebyshev</option> + <option value="correlation">correlation</option> + <option value="dice">dice</option> + <option value="hamming">hamming</option> + <option value="jaccard">jaccard</option> + <option value="kulsinski">kulsinski</option> + <option value="mahalanobis">mahalanobis</option> + <option value="minkowski">minkowski</option> + <option value="rogerstanimoto">rogerstanimoto</option> + <option value="russelrao">russelrao</option> + <option value="seuclidan">seuclidian</option> + <option value="sokalmichener">sokalmichener</option> + <option value="sokalsneath">sokalsneath</option> + <option value="sqeuclidean">sqeuclidean</option> + <option value="yule">yule</option> </param> <param name="random_seed" argument="--random-seed" type="integer" value="0" label="Seed for random number generator"/> </when>