Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 120:5c94a732bd62 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 608485ef08f6221f3247dafe3f8b0ab451871795
author | yhoogstrate |
---|---|
date | Sat, 12 Dec 2015 05:21:15 -0500 |
parents | 0a05f6a91d71 |
children | 6c90a67a13fa |
files | edgeR_Differential_Gene_Expression.xml test-data/Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt |
diffstat | 2 files changed, 68 insertions(+), 19 deletions(-) [+] |
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--- a/edgeR_Differential_Gene_Expression.xml Thu Dec 10 10:34:10 2015 -0500 +++ b/edgeR_Differential_Gene_Expression.xml Sat Dec 12 05:21:15 2015 -0500 @@ -81,6 +81,7 @@ $design_matrix $contrast + $analysis_report_genes $fdr $output_count_edgeR @@ -174,28 +175,29 @@ design_matrix_file <- args[2] contrast <- args[3] -fdr <- args[4] +truncate_table_by_fdr <- args[4] +fdr <- as.double(args[5]) -output_count_edgeR <- args[5] -output_cpm <- args[6] +output_count_edgeR <- args[6] +output_cpm <- args[7] -output_xpkm <- args[7] ##FPKM file - to be implemented +output_xpkm <- args[8] ##FPKM file - to be implemented -output_raw_counts <- args[8] +output_raw_counts <- args[9] -output_MDSplot_logFC <- args[9] -output_MDSplot_logFC_coordinates <- args[10] +output_MDSplot_logFC <- args[10] +output_MDSplot_logFC_coordinates <- args[11] -output_MDSplot_bcv <- args[11] -output_MDSplot_bcv_coordinates <- args[12] +output_MDSplot_bcv <- args[12] +output_MDSplot_bcv_coordinates <- args[13] -output_BCVplot <- args[13] -output_MAplot <- args[14] -output_PValue_distribution_plot <- args[15] -output_hierarchical_clustering_plot <- args[16] -output_heatmap_plot <- args[17] -output_RData_obj <- args[18] -output_format_images <- args[19] +output_BCVplot <- args[14] +output_MAplot <- args[15] +output_PValue_distribution_plot <- args[16] +output_hierarchical_clustering_plot <- args[17] +output_heatmap_plot <- args[18] +output_RData_obj <- args[19] +output_format_images <- args[20] ## Obtain read-counts @@ -388,7 +390,13 @@ lrt <- glmLRT(fit, contrast=cont[,1]) write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout()) - write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA) + + if(truncate_table_by_fdr =="all") { + write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA) + } + else { + write.table(file=output_count_edgeR,subset(topTags(lrt,n=nrow(read_counts))\$table, FDR < fdr),sep="\t",row.names=TRUE,col.names=NA) + } write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA) ## todo EXPORT FPKM @@ -530,7 +538,12 @@ </when> </conditional> - <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" /> + <param name="analysis_report_genes" type="select" label="Report differentially expressed genes"> + <option value="all" selected="true">All genes</option> + <option value="significant">Only significant (defined by FDR cutoff)</option> + </param> + + <param name="fdr" type="float" min="0" max="1" value="0.01" label="False Discovery Rate (FDR) cutoff" help="Used to highlight significant genes in figures" /> <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes"> <option value="make_output_raw_counts">Raw counts table</option> @@ -661,8 +674,36 @@ <param name="contrast" value="E-C"/> + <param name="analysis_report_genes" value="all"/> + <param name="fdr" value="0.01" /> + + <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" /> + </test> + <test> + <param name="analysis_select" value="multi_factor" /> + + <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" /> + <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" /> + + <param name="contrast" value="E-C"/> + + <param name="analysis_report_genes" value="significant"/> <param name="fdr" value="0.05" /> + <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" /> + </test> + <test> + <param name="analysis_select" value="2_factor" /> + + <param name="factorLevel_control" value="C" /> + <param name="countsFile_control" value="Differential_Gene_Expression/C1,Differential_Gene_Expression/C2,Differential_Gene_Expression/C3,Differential_Gene_Expression/C4" ftype="tabular" /> + + <param name="factorLevel_condition" value="E" /> + <param name="countsFile_condition" value="Differential_Gene_Expression/E1,Differential_Gene_Expression/E2,Differential_Gene_Expression/E3,Differential_Gene_Expression/E4" ftype="tabular" /> + + <param name="analysis_report_genes" value="all"/> + <param name="fdr" value="0.01" /> + <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" /> </test> <test> @@ -674,9 +715,10 @@ <param name="factorLevel_condition" value="E" /> <param name="countsFile_condition" value="Differential_Gene_Expression/E1,Differential_Gene_Expression/E2,Differential_Gene_Expression/E3,Differential_Gene_Expression/E4" ftype="tabular" /> + <param name="analysis_report_genes" value="significant"/> <param name="fdr" value="0.05" /> - <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" /> + <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" /> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt Sat Dec 12 05:21:15 2015 -0500 @@ -0,0 +1,7 @@ +"" "genes" "logFC" "logCPM" "LR" "PValue" "FDR" +"15" "RET" 1.94897640107286 13.2940435307943 77.6545995415986 1.22730171935022e-18 3.55917498611563e-17 +"24" "HSPA8" 0.607138087178614 18.9380827005326 16.8408380186893 4.06490891119454e-05 0.000589411792123208 +"12" "IFI44L" -0.665544707287881 11.7020333673755 13.7144720195324 0.000212808308075529 0.00205714697806344 +"10" "MYO18A" -0.608389235629078 14.1586814058554 10.0030349277278 0.00156282461006963 0.0113304784230048 +"4" "DDX11" 0.719283453206409 12.4597575302041 9.1203698809081 0.00252778847312638 0.014661173144133 +"26" "NR2C2AP" 0.538719097450497 12.9331552590697 7.88314604309164 0.00498976028708414 0.0241171747209067