# HG changeset patch
# User recetox
# Date 1755178861 0
# Node ID 8a6c7302de666c080f9c56c803964ba0f13de2cb
# Parent  cd2f3a280463833414b970f5d2186f7d0c5e5c66
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit 01a6a2434c6e77b5061ada328d849a4ad7c30529

diff -r cd2f3a280463 -r 8a6c7302de66 bioconductor_scp.xml
--- a/bioconductor_scp.xml	Wed Jan 22 07:44:00 2025 +0000
+++ b/bioconductor_scp.xml	Thu Aug 14 13:41:01 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bioconductor_scp" name="bioconductor-scp" version="@TOOL_VERSION@+galaxy0" profile="23.0">
+<tool id="bioconductor_scp" name="bioconductor-scp" version="@TOOL_VERSION@+galaxy1" profile="23.0">
     <description>single cell proteomics data analysis workflow</description>
     <macros>
         <import>macros.xml</import>
@@ -417,12 +417,28 @@
             <param name="input_data" value="evidence_subset.txt"/>
             <param name="input_annotations" value="sampleAnnotation.txt"/>
             <param name="runcol" value="19"/>
-            <param name="single_cells" value="Macrophage,Monocyte"/>
-            <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
-            <param name="batch_col" value="2"/>
-            <param name="column_aggregation_peptides" value="6"/>
-            <param name="column_aggregation_proteins" value="17"/>
-            <param name="pca_coloring" value="4"/>
+            <section name="filtering_data">
+                <param name="single_cells" value="Macrophage,Monocyte"/>
+            </section>
+            <section name="peptide_filtering">
+                <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
+            </section>
+            <section name="batch_correction">
+                <conditional name="select_batch_correction">
+                    <param name="batch_col" value="2"/>    
+                </conditional>
+            </section>
+            <section name="peptide_aggregation">
+                <param name="column_aggregation_peptides" value="6"/>
+            </section>
+            <section name="protein_aggregation">
+                <param name="column_aggregation_proteins" value="17"/>
+            </section>
+            <section name="dimensionality_reduction">
+                <conditional name="PCA_computation">
+                    <param name="pca_coloring" value="4"/>
+                </conditional>
+            </section>
             <output name="Processed_data">
                 <assert_contents>
                     <has_n_lines n="90"/>
@@ -435,12 +451,28 @@
             <param name="input_data" value="evidence_subset.txt" />
             <param name="input_annotations" value="sampleAnnotation.txt"/>
             <param name="runcol" value="19"/>
-            <param name="single_cells" value="Macrophage,Monocyte"/>
-            <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
-            <param name="batch_col" value="2"/>
-            <param name="column_aggregation_peptides" value="6"/>
-            <param name="column_aggregation_proteins" value="17"/>
-            <param name="pca_coloring" value="4"/>
+            <section name="filtering_data">
+                <param name="single_cells" value="Macrophage,Monocyte"/>
+            </section>
+            <section name="peptide_filtering">
+                <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
+            </section>
+            <section name="batch_correction">
+                <conditional name="select_batch_correction">
+                    <param name="batch_col" value="2"/>    
+                </conditional>
+            </section>
+            <section name="peptide_aggregation">
+                <param name="column_aggregation_peptides" value="6"/>
+            </section>
+            <section name="protein_aggregation">
+                <param name="column_aggregation_proteins" value="17"/>
+            </section>
+            <section name="dimensionality_reduction">
+                <conditional name="PCA_computation">
+                    <param name="pca_coloring" value="4"/>
+                </conditional>
+            </section>
             <output_collection name="plots" type="list">
                 <element name="PCA" file="PCA.pdf" ftype="pdf" compare="sim_size" delta="60"/>
                 <element name="QC_boxplot_peptide" file="QC_boxplot_peptide.pdf" ftype="pdf" compare="sim_size" delta="40"/>
@@ -465,13 +497,31 @@
             <param name="input_data" value="evidence_subset.txt" />
             <param name="input_annotations" value="sampleAnnotation.txt"/>
             <param name="runcol" value="19"/>
-            <param name="single_cells" value="Macrophage,Monocyte"/>
-            <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
-            <param name="column_aggregation_peptides" value="6"/>
-            <param name="column_aggregation_proteins" value="17"/>
-            <param name="batch_col" value="2"/>
-            <param name="export_tables" value="true"/>
-            <param name="pca_coloring" value="4"/>
+            <section name="filtering_data">
+                <param name="single_cells" value="Macrophage,Monocyte"/>
+            </section>
+            <section name="peptide_filtering">
+                <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
+            </section>
+            <section name="peptide_aggregation">
+                <param name="column_aggregation_peptides" value="6"/>
+            </section>
+            <section name="protein_aggregation">
+                <param name="column_aggregation_proteins" value="17"/>
+            </section>
+            <section name="batch_correction">
+                <conditional name="select_batch_correction">
+                    <param name="batch_col" value="2"/>    
+                </conditional>
+            </section>
+            <section name="data_export">
+                <param name="export_tables" value="true"/>
+            </section>
+            <section name="dimensionality_reduction">
+                <conditional name="PCA_computation">
+                    <param name="pca_coloring" value="4"/>
+                </conditional>
+            </section>
             <output_collection name="intermediate_outputs" type="list" count="6"/>
             <output name="Processed_data">
                 <assert_contents>
@@ -485,14 +535,32 @@
             <param name="input_data" value="evidence_subset.txt" />
             <param name="input_annotations" value="sampleAnnotation.txt"/>
             <param name="runcol" value="19"/>
-            <param name="single_cells" value="Macrophage,Monocyte"/>
-            <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
-            <param name="batch_col" value="2"/>
-            <param name="export_RData" value="TRUE"/>
-            <param name="export_R_script" value="TRUE"/>
-            <param name="column_aggregation_peptides" value="6"/>
-            <param name="column_aggregation_proteins" value="17"/>
-            <param name="pca_coloring" value="4"/>
+            <section name="filtering_data">
+                <param name="single_cells" value="Macrophage,Monocyte"/>
+            </section>
+            <section name="peptide_filtering">
+                <param name="samples_to_keep" value="Macrophage,Monocyte,Blank"/>
+            </section>
+            <section name="batch_correction">
+                <conditional name="select_batch_correction">
+                    <param name="batch_col" value="2"/>    
+                </conditional>
+            </section>
+            <section name="peptide_aggregation">
+                <param name="column_aggregation_peptides" value="6"/>
+            </section>
+            <section name="protein_aggregation">
+                <param name="column_aggregation_proteins" value="17"/>
+            </section>
+            <section name="data_export">
+                <param name="export_RData" value="TRUE"/>
+                <param name="export_R_script" value="TRUE"/>
+            </section>
+            <section name="dimensionality_reduction">
+                <conditional name="PCA_computation">
+                    <param name="pca_coloring" value="4"/>
+                </conditional>
+            </section>
             <output name="Processed_data">
                 <assert_contents>
                     <has_size size="625000" delta="20"/>
diff -r cd2f3a280463 -r 8a6c7302de66 macros.xml
--- a/macros.xml	Wed Jan 22 07:44:00 2025 +0000
+++ b/macros.xml	Thu Aug 14 13:41:01 2025 +0000
@@ -56,7 +56,7 @@
                 <options from_dataset="input_annotations">
                     <column name="name" index="3"/>
                     <column name="value" index="3"/>
-                    <filter type="unique_value" name="unique" column="3"/>
+                    <filter type="unique_value" column="3"/>
                 </options>
             </param>
             <param name="SCR_threshold" type="float" value="0.1" min="0" max="1" label="Mean SCR threshold" help="Mean sample-to-carrier (SCR) threshold. 0.1 corresponds to 10%."/> 
@@ -81,7 +81,7 @@
                 <options from_dataset="input_annotations">
                     <column name="name" index="3"/>
                     <column name="value" index="3"/>
-                    <filter type="unique_value" name="unique" column="3"/>
+                    <filter type="unique_value" column="3"/>
                 </options>
             </param>
             <conditional name="filter_median_intensity">