Mercurial > repos > iuc > deseq2
changeset 24:71bacea10eee draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
| author | iuc |
|---|---|
| date | Sat, 29 Feb 2020 17:08:08 -0500 |
| parents | 0696db066a5b |
| children | de44f8eff84a |
| files | deseq2.R deseq2.xml |
| diffstat | 2 files changed, 41 insertions(+), 3 deletions(-) [+] |
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--- a/deseq2.R Tue Mar 26 06:25:00 2019 -0400 +++ b/deseq2.R Sat Feb 29 17:08:08 2020 -0500 @@ -354,7 +354,7 @@ outDF <- as.data.frame(resSorted) outDF$geneID <- rownames(outDF) outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")] - filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref) + filename <- paste0(primaryFactor,"_",lvl,"_vs_",ref) write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE) if (independentFiltering) { threshold <- unname(attr(res, "filterThreshold"))
--- a/deseq2.xml Tue Mar 26 06:25:00 2019 -0400 +++ b/deseq2.xml Sat Feb 29 17:08:08 2020 -0500 @@ -1,4 +1,4 @@ -<tool id="deseq2" name="DESeq2" version="2.11.40.6"> +<tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1"> <description>Determines differentially expressed features from count tables</description> <macros> <import>deseq2_macros.xml</import> @@ -217,7 +217,7 @@ </data> <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> <filter>many_contrasts is True</filter> - <discover_datasets pattern="None.(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> + <discover_datasets pattern="(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> </collection> <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> <filter>pdf == True</filter> @@ -445,6 +445,44 @@ </assert_contents> </output> </test> + <!--Ensure many_contrasts produces output collection --> + <test expect_num_outputs="1"> + <param name="select_data|how" value="group_tags"/> + <param name="select_data|countsFile"> + <collection type="list"> + <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/> + <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/> + <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/> + <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/> + <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/> + <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/> + </collection> + </param> + <repeat name="rep_factorName"> + <param name="factorName" value="Treatment"/> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="groups" value="primary:treated"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="groups" value="primary:untreated"/> + </repeat> + </repeat> + <param name="pdf" value="False"/> + <param name="tximport_selector" value="tximport"/> + <param name="txtype" value="sailfish"/> + <param name="mapping_format_selector" value="tabular"/> + <param name="tabular_file" value="tx2gene.tab"/> + <param name="many_contrasts" value="true"/> + <output_collection name="split_output" type="list" count="1"> + <element name="Treatment_Treated_vs_Untreated"> + <assert_contents> + <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ .. class:: infomark