changeset 3:d30ef0613122 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/squidpy commit 3c79b731a6c4379bfb0491ceebf767789c8b79c4

--- 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" />