Mercurial > repos > iuc > deseq2
changeset 33:6c363db8c702 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 commit 8f0f0f51f30cc630daebfeae8acae93e84dbd35c
| author | iuc |
|---|---|
| date | Tue, 06 Jan 2026 11:22:33 +0000 |
| parents | 2275d0688bca |
| children | |
| files | deseq2.R deseq2.xml macros.xml test-data/sample_sheet_numeric.tab |
| diffstat | 4 files changed, 49 insertions(+), 2 deletions(-) [+] |
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--- a/deseq2.R Fri Dec 19 08:09:52 2025 +0000 +++ b/deseq2.R Tue Jan 06 11:22:33 2026 +0000 @@ -244,7 +244,8 @@ # Find matching row in sample sheet matching_row <- which(sample_sheet[[sample_id_col]] == element_id) if (length(matching_row) > 0) { - level <- sample_sheet[[factor_name]][matching_row[1]] + # Convert level to character to ensure consistent list indexing + level <- as.character(sample_sheet[[factor_name]][matching_row[1]]) if (!(level %in% names(level_to_files))) { level_to_files[[level]] <- character(0) level_order <- c(level_order, level) # Record order of first appearance
--- a/deseq2.xml Fri Dec 19 08:09:52 2025 +0000 +++ b/deseq2.xml Tue Jan 06 11:22:33 2026 +0000 @@ -983,6 +983,44 @@ </assert_contents> </output> </test> + <!--Test sample_sheet_contrasts with numeric factor column in design formula --> + <test expect_num_outputs="2"> + <param name="select_data|how" value="sample_sheet_contrasts"/> + <param name="select_data|countsFile"> + <collection type="list"> + <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/> + <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/> + <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/> + <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/> + <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/> + <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/> + <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/> + </collection> + </param> + <param name="select_data|sample_sheet" value="sample_sheet_numeric.tab"/> + <param name="select_data|design_formula_mode|mode" value="custom"/> + <param name="select_data|design_formula_mode|design_formula" value="~ replicate + treatment"/> + <param name="select_data|design_formula_mode|reference_level" value="Untreated"/> + <section name="advanced_options"> + <param name="use_beta_priors" value="1"/> + </section> + <section name="output_options"> + <param name="output_selector" value="normCounts"/> + </section> + <output name="counts_out"> + <assert_contents> + <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/> + <has_n_columns n="8"/> + </assert_contents> + </output> + <output name="deseq_out"> + <assert_contents> + <!-- Multi-factor design with numeric replicate column --> + <has_text_matching expression="FBgn0003360\t1933\.950.*"/> + <has_n_lines n="3999"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ .. class:: infomark
--- a/macros.xml Fri Dec 19 08:09:52 2025 +0000 +++ b/macros.xml Tue Jan 06 11:22:33 2026 +0000 @@ -39,7 +39,7 @@ </xml> <token name="@TOOL_VERSION@">2.11.40.8</token> <token name="@DESEQ2_VERSION@">1.40.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> <xml name="edam_ontology"> <edam_topics>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_sheet_numeric.tab Tue Jan 06 11:22:33 2026 +0000 @@ -0,0 +1,8 @@ +sample treatment replicate +GSM461179_treat_single.counts Treated 1 +GSM461180_treat_paired.counts Treated 2 +GSM461181_treat_paired.counts Treated 3 +GSM461176_untreat_single.counts Untreated 1 +GSM461177_untreat_paired.counts Untreated 2 +GSM461178_untreat_paired.counts Untreated 3 +GSM461182_untreat_single.counts Untreated 4