Mercurial > repos > ebi-gxa > score_genes_aucell
diff decoupler_aucell_score.xml @ 1:e024d8280886 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
author | ebi-gxa |
---|---|
date | Thu, 16 Nov 2023 20:05:21 +0000 |
parents | 1e8697931d73 |
children | e887a7e8c5b4 |
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--- a/decoupler_aucell_score.xml Thu Nov 09 11:36:08 2023 +0000 +++ b/decoupler_aucell_score.xml Thu Nov 16 20:05:21 2023 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy0" profile="20.05"> +<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05"> <description> scores cells using the AUCell method for gene sets. </description> @@ -10,11 +10,13 @@ python '$__tool_directory__/decoupler_aucell_score.py' --input_file '$input_file' #if $gene_lists_source.source == "gmt" - --gmt_file '$gmt_file' - --gene_sets_to_score '$gene_sets_to_score' + --gmt_file '$gene_lists_source.gmt_file' + #if $gene_lists_source.gene_sets_to_score + --gene_sets_to_score '$gene_lists_source.gene_sets_to_score' + #end if #else: - --gene_lists_to_score '$gene_lists_to_score' - --score_names '$score_names' + --gene_lists_to_score '$gene_lists_source.gene_lists_to_score' + --score_names '$gene_lists_source.score_names' #end if --gene_symbols_field '$gene_symbols_field' $use_raw @@ -34,7 +36,7 @@ </param> <when value="gmt"> <param name="gmt_file" type="data" format="txt" label="GMT file with gene sets" /> - <param name="gene_sets_to_score" type="text" label="Gene sets to score within the GMT file" /> + <param name="gene_sets_to_score" type="text" optional="true" label="Gene sets to score within the GMT file" /> </when> <when value="enumerated"> <param name="gene_lists_to_score" type="text" label="Genes to score" /> @@ -56,11 +58,11 @@ <tests> <test expect_num_outputs="1"> <param name="input_file" value="mito_counted_anndata.h5ad"/> - <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> - <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> <param name="gene_symbols_field" value="Symbol"/> <param name="write_anndata" value="true"/> <conditional name="gene_lists_source"> + <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> + <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> <param name="source" value="gmt"/> </conditional> <output name="output_ad"> @@ -72,12 +74,27 @@ </test> <test expect_num_outputs="1"> <param name="input_file" value="mito_counted_anndata.h5ad"/> - <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/> - <param name="score_names" value="TCell,Macro"/> + <param name="gene_symbols_field" value="Symbol"/> + <param name="write_anndata" value="true"/> + <conditional name="gene_lists_source"> + <param name="source" value="gmt"/> + <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> + </conditional> + <output name="output_ad"> + <assert_contents> + <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> + <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_file" value="mito_counted_anndata.h5ad"/> <param name="gene_symbols_field" value="Symbol"/> <param name="write_anndata" value="true"/> <conditional name="gene_lists_source"> <param name="source" value="enumerated"/> + <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/> + <param name="score_names" value="TCell,Macro"/> </conditional> <output name="output_ad"> <assert_contents> @@ -88,12 +105,12 @@ </test> <test expect_num_outputs="1"> <param name="input_file" value="mito_counted_anndata.h5ad"/> - <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> - <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> <param name="gene_symbols_field" value="Symbol"/> <param name="write_anndata" value="False"/> <conditional name="gene_lists_source"> <param name="source" value="gmt"/> + <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> + <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> </conditional> <output name="output_table"> <assert_contents>