Mercurial > repos > recetox > bioconductor_scp
changeset 1:8a6c7302de66 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/bioconductor-scp commit 01a6a2434c6e77b5061ada328d849a4ad7c30529
| author | recetox |
|---|---|
| date | Thu, 14 Aug 2025 13:41:01 +0000 |
| parents | cd2f3a280463 |
| children | |
| files | bioconductor_scp.xml macros.xml |
| diffstat | 2 files changed, 98 insertions(+), 30 deletions(-) [+] |
line wrap: on
line diff
--- 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"/>
--- 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">