| Previous changeset 22:a30d21fd5319 (2021-07-22) Next changeset 24:7779b9dcf040 (2021-08-03) |
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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 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty" |
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modified:
scanpy-neighbours.xml |
| b |
| diff -r a30d21fd5319 -r bc9e8de21efb scanpy-neighbours.xml --- a/scanpy-neighbours.xml Thu Jul 22 20:57:34 2021 +0000 +++ b/scanpy-neighbours.xml Fri Jul 23 08:28:48 2021 +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@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>to derive kNN graph</description> <macros> <import>scanpy_macros2.xml</import> @@ -31,7 +31,7 @@ --method '${settings.method}' --metric '${settings.metric}' --random-state '${settings.random_seed}' - #if $settings.use_rep != "auto" + #if $settings.use_rep --use-rep '${settings.use_rep}' #end if #if $settings.n_pcs @@ -55,11 +55,7 @@ <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="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> - <option value="X_diffmap"> X_diffmap, use diffusion map</option> - </param> + <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."/> <param name="n_pcs" argument="--n-pcs" type="integer" value="50" optional="true" label="Number of PCs to use"/> <param name="knn" argument="--knn" type="boolean" truevalue="" falsevalue="--no-knn" checked="true" label="Use hard threshold to restrict neighbourhood size (otherwise use a Gaussian kernel to down weight distant neighbors)"/> |