# HG changeset patch # User iuc # Date 1743233844 0 # Node ID 923dcc644832938f6c89d96847aaa44f5ec629ef # Parent 13cf83ced60ce17c92ebcd5b1f81f7a839e45c52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 08ce25c9b0ae236d3c0c352119de9db6b56c2925 diff -r 13cf83ced60c -r 923dcc644832 import.xml --- a/import.xml Sat Jan 11 21:11:06 2025 +0000 +++ b/import.xml Sat Mar 29 07:37:24 2025 +0000 @@ -1,4 +1,4 @@ - + from different formats macros.xml @@ -85,6 +85,26 @@ #else if $in.adata_format == 'umi_tools' adata = ad.read_umi_tools('umi_tools_input.gz') + +#else if $in.adata_format == 'custom' +import pandas as pd + +adata = ad.read_mtx(filename='$in.mtx') +adata = adata.transpose().copy() + +obs = pd.read_csv('$in.obs', sep='\t', index_col=0) +var = pd.read_csv('$in.var', sep='\t', index_col=0) + +if adata.shape[0] != obs.shape[0]: + raise ValueError(f"Mismatch: adata has {adata.shape[0]} cells, but obs has {obs.shape[0]} rows.") + +if adata.shape[1] != var.shape[0]: + raise ValueError(f"Mismatch: adata has {adata.shape[1]} genes, but var has {var.shape[0]} rows.") + + +adata.obs = obs +adata.var = var + #end if adata.write('anndata.h5ad', compression='gzip') print(adata) @@ -98,6 +118,7 @@ + @@ -136,6 +157,11 @@ + + + + + @@ -273,6 +299,22 @@ + + + + + + + + + + + + + + + +