Mercurial > repos > ebi-gxa > decoupler_pseudobulk
changeset 9:bd4b54b75888 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
| author | ebi-gxa |
|---|---|
| date | Sun, 15 Sep 2024 09:56:34 +0000 |
| parents | 93f61ea19336 |
| children | f6040492b499 |
| files | decoupler_pseudobulk.py decoupler_pseudobulk.xml |
| diffstat | 2 files changed, 16 insertions(+), 1 deletions(-) [+] |
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--- a/decoupler_pseudobulk.py Mon Jul 15 10:56:42 2024 +0000 +++ b/decoupler_pseudobulk.py Sun Sep 15 09:56:34 2024 +0000 @@ -320,6 +320,21 @@ min_counts=args.min_counts, ) + print("Created pseudo-bulk AnnData, checking if fields still make sense.") + print( + "If this fails this check, it might mean that you asked for factors " + + "that are not compatible with you sample identifiers (ie. asked for " + + "phase in the factors, but each sample contains more than one phase, " + + "try joining fields)" + ) + if factor_fields: + check_fields( + factor_fields, + pseudobulk_data, + context=" after creation of pseudo-bulk AnnData", + ) + print("Factors requested are adequate for the pseudo-bulked AnnData!") + # Plot pseudobulk samples plot_pseudobulk_samples( pseudobulk_data,
--- a/decoupler_pseudobulk.xml Mon Jul 15 10:56:42 2024 +0000 +++ b/decoupler_pseudobulk.xml Sun Sep 15 09:56:34 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy3" profile="20.05"> +<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy4" profile="20.05"> <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description> <requirements> <requirement type="package" version="1.4.0">decoupler</requirement>