Mercurial > repos > ebi-gxa > scanpy_run_tsne
changeset 22:8b0d6f6f44c8 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4332e90fa9f269bf4a8b912366eeace9c040b4c4-dirty"
| author | ebi-gxa |
|---|---|
| date | Fri, 23 Jul 2021 08:32:50 +0000 |
| parents | c4868b59cf7f |
| children | 3fb53f5e46ea |
| files | scanpy-run-tsne.xml |
| diffstat | 1 files changed, 3 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/scanpy-run-tsne.xml Thu Jul 22 20:56:08 2021 +0000 +++ b/scanpy-run-tsne.xml Fri Jul 23 08:32:50 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> +<tool id="scanpy_run_tsne" name="Scanpy RunTSNE" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> <description>visualise cell clusters using tSNE</description> <macros> <import>scanpy_macros2.xml</import> @@ -9,7 +9,7 @@ #set embeddings_tsv='embeddings.tsv' ln -s '${input_obj_file}' input.h5 && PYTHONIOENCODING=utf-8 scanpy-run-tsne -#if $use_rep != "auto" +#if $use_rep --use-rep '${use_rep}' #end if #if $embeddings @@ -64,11 +64,7 @@ <expand macro="output_object_params"/> <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/> - <param name="use_rep" argument="--use-rep" type="select" label="Use the indicated representation"> - <option value="X_pca">X_pca, use PCs</option> - <option value="X">X, use normalised expression values</option> - <option value="auto" selected="true">Automatically chosen based on problem size</option> - </param> + <param name="use_rep" argument="--use-rep" type="text" optional="true" label="Use the indicated representation" help="Use the indicated representation. 'X' (for the content of .X, usuaally 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."/> <conditional name="settings"> <param name="default" type="boolean" checked="true" label="Use programme defaults"/> <when value="true"/>