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protein aggregation column done via select, not a text
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KristinaGomoryova committed Jan 8, 2025
1 parent 1799c28 commit 5757ba0
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Showing 2 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion tools/scp/macros.xml
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<param name = "aggregation_proteins" type="select" label="Which function to use for the aggregation?" help= "How to aggregate peptides to proteins?">
<expand macro="aggregation_options"/>
</param>
<param name="column_aggregation_proteins" type="text" value="Leading.razor.protein" label="Which column should be used for the peptide to protein aggregation?" optional="false" help="Which column should be used for the peptide to protein aggregation."/>
<param name="column_aggregation_proteins" type="data_column" data_ref="input_data" use_header_names="true" label="Which column should be used for the peptide to protein aggregation?" help="Which column should be used for the peptide to protein aggregation. Leading.razor.protein is recommended."/>
</section>

<section name="protein_processing" title="Processing protein data" expanded="true">
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4 changes: 2 additions & 2 deletions tools/scp/scp_workflow.xml
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Expand Up @@ -121,7 +121,6 @@
#end if
## aggregation_fun <- match.fun("${peptide_aggregation.aggregation_peptides}")
## print("${peptide_aggregation.column_aggregation_peptides}")
fcol_aggregation <- colnames(data_input)[${peptide_aggregation.column_aggregation_peptides}]
scp <- aggregateFeaturesOverAssays(scp,
i = 1:number_of_assays,
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#end if
## aggregation_fun_prot <- match.fun("${protein_aggregation.aggregation_proteins}")
fcol_aggregation <- colnames(data_input)[${protein_aggregation.column_aggregation_proteins}]
scp <- aggregateFeatures(scp,
i = "peptides_log",
name = "proteins",
fcol = "${protein_aggregation.column_aggregation_proteins}",
fcol = fcol_aggregation,
fun = ${protein_aggregation.aggregation_proteins}, na.rm = TRUE)
#if $protein_processing.normalization_method_protein.choose_normalization_protein == "simple_prot"
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