| Previous changeset 11:232937b5bb8f (2020-06-05) Next changeset 13:e6c989a9211c (2020-09-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty" |
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modified:
scanpy-neighbours.xml scanpy_macros2.xml |
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| diff -r 232937b5bb8f -r c78c930e3263 scanpy-neighbours.xml --- a/scanpy-neighbours.xml Fri Jun 05 09:12:59 2020 -0400 +++ b/scanpy-neighbours.xml Mon Sep 07 14:02:36 2020 +0000 |
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| @@ -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> |
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| diff -r 232937b5bb8f -r c78c930e3263 scanpy_macros2.xml --- a/scanpy_macros2.xml Fri Jun 05 09:12:59 2020 -0400 +++ b/scanpy_macros2.xml Mon Sep 07 14:02:36 2020 +0000 |
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| @@ -1,10 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">1.4.3</token> + <token name="@TOOL_VERSION@">1.6.0</token> <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token> <token name="@PROFILE@">18.01</token> <token name="@VERSION_HISTORY@"><![CDATA[ **Version history** +1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home at +EMBL-EBI https://www.ebi.ac.uk/ + 1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca. 1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes. @@ -46,7 +49,7 @@ <xml name="requirements"> <requirements> - <requirement type="package" version="0.2.10">scanpy-scripts</requirement> + <requirement type="package" version="0.3.0">scanpy-scripts</requirement> <yield/> </requirements> </xml> |