Mercurial > repos > goeckslab > squidpy
changeset 3:d30ef0613122 draft
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 3c79b731a6c4379bfb0491ceebf767789c8b79c4
| author | goeckslab |
|---|---|
| date | Tue, 14 May 2024 21:54:05 +0000 |
| parents | 4a058bd23a12 |
| children | 11ea000ad53f |
| files | main_macros.xml squidpy_spatial.py squidpy_spatial.xml |
| diffstat | 3 files changed, 2 insertions(+), 16 deletions(-) [+] |
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--- a/main_macros.xml Mon Apr 29 20:42:57 2024 +0000 +++ b/main_macros.xml Tue May 14 21:54:05 2024 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.4.1</token> <token name="@PROFILE@">20.01</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="macro_stdio"> <stdio>
--- a/squidpy_spatial.py Mon Apr 29 20:42:57 2024 +0000 +++ b/squidpy_spatial.py Tue May 14 21:54:05 2024 +0000 @@ -51,11 +51,6 @@ options[k] = [e.strip() for e in v.split(',')] elif k == 'radius': # for spatial_neighbors options[k] = ast.literal_eval(v) - elif k == 'numba_parallel': # for nhood_enrichment and ligrec - if v == 'false': - options[k] = False - elif v == 'true': - options[k] = True elif k == 'interactions': # for ligrec options[k] = pd.read_csv(v, sep="\t") elif k == 'max_neighs':
--- a/squidpy_spatial.xml Mon Apr 29 20:42:57 2024 +0000 +++ b/squidpy_spatial.xml Tue May 14 21:54:05 2024 +0000 @@ -11,6 +11,7 @@ <version_command>echo "@TOOL_VERSION@"</version_command> <command detect_errors="aggressive"> <![CDATA[ + export TQDM_DISABLE=True && python '$__tool_directory__/squidpy_spatial.py' --inputs '$inputs' --anndata '$anndata' @@ -64,11 +65,6 @@ <expand macro="squidpy_spatial_options"> <param argument="connectivity_key" type="text" value="" optional="true" label="Key in anndata.AnnData.obsp where spatial connectivities are stored" /> <param argument="n_perms" type="integer" value="1000" label="Number of permutations for the permutation test" /> - <param argument="numba_parallel" type="select" label="Whether to use numba.prange or not"> - <option value="false" selected="true">No -- Recommended for small datasets or small number of interactions</option> - <option value="true">Yes</option> - <option value="none">Auto</option> - </param> <param argument="seed" type="integer" value="" optional="true" label="Randomness seed" /> </expand> <expand macro="squidpy_plotting_options_more"> @@ -181,11 +177,6 @@ <option value="clusters" selected="true">clusters -- correct clusters by performing FDR correction across the interactions</option> <option value="interactions">interactions -- correct interactions by performing FDR correction across the clusters</option> </param> - <param argument="numba_parallel" type="select" label="Whether to use numba.prange or not"> - <option value="false" selected="true">No -- Recommended for small datasets or small number of interactions</option> - <option value="true">Yes</option> - <option value="none">Auto</option> - </param> <param argument="key_added" type="text" value="" optional="true" label="Key in anndata to store the result" help="In `anndata.AnnData.uns`. If None, '{cluster_key}_ligrec' will be used." /> <param argument="gene_symbols" type="text" value="" optional="true" label="Key in anndata.AnnData.var to use instead of anndata.AnnData.var_names" help="Optional." /> <param argument="seed" type="integer" value="" label="Randomness seed" />