| Previous changeset 1:046d8ff974ff (2023-09-27) Next changeset 3:4fa5f370599f (2023-11-09) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 85a3118a571246d88aaad26733d0c62009cb736b |
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modified:
decoupler_pseudobulk.py decoupler_pseudobulk.xml |
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| diff -r 046d8ff974ff -r 130e25d3ce92 decoupler_pseudobulk.py --- a/decoupler_pseudobulk.py Wed Sep 27 01:11:32 2023 +0000 +++ b/decoupler_pseudobulk.py Fri Oct 13 15:19:51 2023 +0000 |
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| @@ -165,9 +165,11 @@ # Merge adata.obs fields specified in args.adata_obs_fields_to_merge if args.adata_obs_fields_to_merge: - fields = args.adata_obs_fields_to_merge.split(",") - check_fields(fields, adata) - adata = merge_adata_obs_fields(fields, adata) + # first split potential groups by ":" and iterate over them + for group in args.adata_obs_fields_to_merge.split(":"): + fields = group.split(",") + check_fields(fields, adata) + adata = merge_adata_obs_fields(fields, adata) check_fields([args.groupby, args.sample_key], adata) @@ -274,7 +276,7 @@ "-m", "--adata_obs_fields_to_merge", type=str, - help="Fields in adata.obs to merge, comma separated", + help="Fields in adata.obs to merge, comma separated. You can have more than one set of fields, separated by semi-colon ;", ) parser.add_argument( "--groupby", |
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| diff -r 046d8ff974ff -r 130e25d3ce92 decoupler_pseudobulk.xml --- a/decoupler_pseudobulk.xml Wed Sep 27 01:11:32 2023 +0000 +++ b/decoupler_pseudobulk.xml Fri Oct 13 15:19:51 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy1" profile="20.05"> +<tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy2" 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> @@ -8,14 +8,14 @@ mkdir plots_output_dir && python '$__tool_directory__/decoupler_pseudobulk.py' $input_file #if $adata_obs_fields_to_merge: - --adata_obs_fields_to_merge $adata_obs_fields_to_merge + --adata_obs_fields_to_merge '$adata_obs_fields_to_merge' #end if - --groupby $groupby - --sample_key $sample_key + --groupby '$groupby' + --sample_key '$sample_key' #if $layer: - --layer $layer + --layer '$layer' #end if - --mode $mode + --mode '$mode' #if $use_raw: --use_raw #end if @@ -32,7 +32,7 @@ --min_total_counts $min_total_counts #end if #if $produce_anndata: - --anndata_output_path $pbulk_anndata + --anndata_output_path '$pbulk_anndata' #end if #if $filter_expr: --filter_expr @@ -50,7 +50,7 @@ </environment_variables> <inputs> <param type="data" name="input_file" format="data" label="Input AnnData file"/> - <param type="text" name="adata_obs_fields_to_merge" label="Obs Fields to Merge" optional="true" help="Fields in adata.obs to merge, comma separated (optional). They will be available as field1_field2_field3 in the AnnData Obs dataframe."/> + <param type="text" name="adata_obs_fields_to_merge" label="Obs Fields to Merge" optional="true" help="Fields in adata.obs to merge, comma separated (optional). They will be available as field1_field2_field3 in the AnnData Obs dataframe. You can have multiple groups to merge, separated by colon (:)."/> <param type="text" name="groupby" label="Groupby column" help="The column in adata.obs that defines the groups. Merged columns in the above field are available here."/> <param type="text" name="sample_key" label="Sample Key column" help="The column in adata.obs that defines the samples. Merged columns in the above field are available here."/> <param type="text" name="layer" label="Layer" optional="true" help="The name of the layer of the AnnData object to use. It needs to be present in the AnnData object."/> @@ -87,7 +87,7 @@ <tests> <test expect_num_outputs="6"> <param name="input_file" value="mito_counted_anndata.h5ad"/> - <param name="adata_obs_fields_to_merge" value="batch,sex"/> + <param name="adata_obs_fields_to_merge" value="batch,sex:batch,genotype"/> <param name="groupby" value="batch_sex"/> <param name="sample_key" value="genotype"/> <param name="factor_fields" value="genotype,batch_sex"/> |