edger_with_design_matrix: edgeR_Differential_Gene

comparison edgeR_Differential_Gene_Expression.xml @ 5:bde663b872d9 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc

author	yhoogstrate
date	Mon, 14 Dec 2015 11:01:38 -0500
parents	5d38abf7e4b6
children	31a23ae7c61e

comparison

equal deleted inserted replaced

-:5d38abf7e4b6
+:bde663b872d9
 description="LOCALE has not been set correctly" />
 </stdio>
 <version_command>echo $(R --version | grep version | grep -v GNU)", EdgeR version" $(R --vanilla --slave -e "library(edgeR) ; cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2&gt; /dev/null | grep -v -i "WARNING: ")</version_command>
-<command>
+<command><![CDATA[
+#if $analysis_type.analysis_select == "multi_factor"
+#set $expression_matrix = $analysis_type.expression_matrix
+#set $design_matrix = $analysis_type.design_matrix
+#set $contrast = $analysis_type.contrast
+#else
+## Design and Expression matrices do not exist - create them
+#set $expression_matrix = "expression_matrix.txt"
+#set $design_matrix = "design_matrix.txt"
+#set $contrast = str($analysis_type.factorLevel_condition)+"-"+str($analysis_type.factorLevel_control)
+## -- Create expression matrix
+cut -f 1 "$analysis_type.countsFile_control[1]" > gene_ids.column.txt &&
+#for $file in $analysis_type.countsFile_control:
+cut -f 2 "${file}" > "${file}.expression_column.txt"    &&
+#end for
+#for $file in $analysis_type.countsFile_condition:
+cut -f 2 "${file}" > "${file}.expression_column.txt"    &&
+#end for
+paste
+gene_ids.column.txt
+#for $file in $analysis_type.countsFile_control:
+"${file}.expression_column.txt"
+#end for
+#for $file in $analysis_type.countsFile_condition:
+"${file}.expression_column.txt"
+#end for
+> "${expression_matrix}"                                &&
+## -- Create design matrix matrix
+echo "sample-name	Condition" >> ${design_matrix}          &&
+#for $file in $analysis_type.countsFile_control:
+echo "${file.name}	${analysis_type.factorLevel_control}" >> ${design_matrix}        &&
+#end for
+#for $file in $analysis_type.countsFile_condition:
+echo "${file.name}	${analysis_type.factorLevel_condition}" >> ${design_matrix}      &&
+#end for
+#end if
 R --vanilla --slave -f $R_script '--args
 $expression_matrix
 $design_matrix
 $contrast
+$analysis_report_genes
 $fdr
 $output_count_edgeR
 $output_cpm
-/dev/null                                                    <!-- Calculation of FPKM/RPKM should come here -->
+/dev/null                                                   ### Calculation of FPKM/RPKM should come here
 #if $output_raw_counts:
 $output_raw_counts
 #else:
 /dev/null
 /dev/null
 #end if
 $output_format_images
 '
+]]>
 </command>
 <configfiles>
 <configfile name="R_script">
 <![CDATA[
 expression_matrix_file              <- args[1]
 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_BCVplot                      <- args[14]
-output_PValue_distribution_plot     <- args[15]
+output_MAplot                       <- args[15]
-output_hierarchical_clustering_plot <- args[16]
+output_PValue_distribution_plot     <- args[16]
-output_heatmap_plot                 <- args[17]
+output_hierarchical_clustering_plot <- args[17]
-output_RData_obj                    <- args[18]
+output_heatmap_plot                 <- args[18]
-output_format_images                <- args[19]
+output_RData_obj                    <- args[19]
+output_format_images                <- args[20]
 ## Obtain read-counts
 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
 colnames(design_matrix) <- make.names(colnames(design_matrix))
 for(i in 1:ncol(design_matrix)) {
 old <- design_matrix[,i]
-design_matrix[,i] <- make.names(design_matrix[,i])
-if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
+if(any(grepl("^[0-9]+$", old, perl=TRUE) == FALSE)){
-print("Renaming of factors:")
+# Convert invalid names
-print(old)
+design_matrix[,i] <- make.names(design_matrix[,i])
-print("To:")
-print(design_matrix[,i])
+# Print if names have been converted
-}
+if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
-## The following line seems to malfunction the script:
+print("Renamed of factors:")
-##design_matrix[,i] <- as.factor(design_matrix[,i])
+print(old)
+print("To:")
+print(design_matrix[,i])
+}
+} else {
+# Only numerical factors: these are blocking / pairing factors
+design_matrix[,i] <- as.numeric(design_matrix[,i])
+}
 }
 ## 1) In the expression matrix, you only want to have the samples described in the design matrix
 columns <- match(rownames(design_matrix),colnames(expression_matrix))
 columns <- columns[!is.na(columns)]
 cont <- c(contrast)
 cont <- makeContrasts(contrasts=cont, levels=design)
 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
 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
 ]]>
 </configfile>
 </configfiles>
 <inputs>
-<param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" />
+<conditional name="analysis_type">
-<param name="design_matrix" type="data" format="tabular" label="Design matrix" help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." />
+<param name="analysis_select" type="select" label="Analysis type">
+<option value="2_factor" selected="true">2-Group test</option>
-<param name="contrast" type="text" label="Contrast (biological question)" help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info: http://www.bioconductor.org/packages/release/bioc/html/limma.html and http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf." />
+<option value="multi_factor">Multigroup test and/or complex designs with e.g. blocking</option>
+</param>
-<param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" />
+<when value="2_factor">
+<param name="factorLevel_control" type="text" value="Control"
+label="Specify a factor level" help="Only letters, numbers and underscores will be retained in this field">
+<sanitizer>
+<valid initial="string.letters,string.digits"><add value="_" /></valid>
+</sanitizer>
+</param>
+<param name="countsFile_control" type="data" format="tabular,csv" multiple="true" label="Counts file(s)"/>
+<param name="factorLevel_condition" type="text" value="Condition"
+label="Specify a factor level" help="Only letters, numbers and underscores will be retained in this field">
+<sanitizer>
+<valid initial="string.letters,string.digits"><add value="_" /></valid>
+</sanitizer>
+</param>
+<param name="countsFile_condition" type="data" format="tabular,csv" multiple="true" label="Counts file(s)"/>
+</when>
+<when value="multi_factor">
+<param name="expression_matrix" type="data" format="tabular,csv" label="Expression (read count) matrix" />
+<param name="design_matrix" type="data" format="tabular,csv" label="Design matrix"
+help="Ensure your samplenames are identical to those in the expression matrix. Preferentially, create the contrast matrix using 'edgeR: Design- from Expression matrix'." />
+<param name="contrast" type="text" label="Contrast (biological question)"
+help="e.g. 'tumor-normal' or '(G1+G2)/2-G3' using the factors chosen in the design matrix. Read the 'makeContrasts' manual from Limma package for more info: http://www.bioconductor.org/packages/release/bioc/html/limma.html and http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf." />
+</when>
+</conditional>
+<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>
 <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option>
 <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option>
 </param>
 <param name="output_format_images" type="select" label="Output format of images" display="radio">
 <option value="png">Portable network graphics (.png)</option>
 <option value="pdf">Portable document format (.pdf)</option>
-<option value="svg">Scalable vector graphics (.svg)</option>
+<option value="svg" selected="true">Scalable vector graphics (.svg)</option>
 </param>
 </inputs>
 <outputs>
-<data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
+<data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${on_string}: differentially expressed genes" >
-<data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
+<actions>
+<action name="column_names" type="metadata" default="original_gene_position,genes,logFC,logCPM,LR,PValue,FDR" />
-<data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
+</actions>
+</data>
+<data format="tabular" name="output_cpm" label="edgeR DGE on ${on_string}: CPM" />
+<data format="tabular" name="output_raw_counts" label="edgeR DGE on ${on_string}: raw counts">
 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
 </data>
-<data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (logFC method)">
+<data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${on_string}: MDS-plot (logFC method)">
 <filter>outputs and ("make_output_MDSplot_logFC" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (logFC method)">
+<data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${on_string}: MDS-plot coordinates table (logFC method)">
 <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter>
 </data>
-<data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)">
+<data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${on_string}: MDS-plot (bcv method)">
 <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (BCV method)">
+<data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${on_string}: MDS-plot coordinates table (BCV method)">
 <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter>
 </data>
-<data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
+<data format="png" name="output_BCVplot" label="edgeR DGE on ${on_string}: BCV-plot">
 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="png" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
+<data format="png" name="output_MAplot" label="edgeR DGE on ${on_string}: MA-plot">
 <filter>outputs and ("make_output_MAplot" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
+<data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${on_string}: P-Value distribution">
 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
+<data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${on_string}: Hierarchical custering">
 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
+<data format="png" name="output_heatmap_plot" label="edgeR DGE on ${on_string}: Heatmap">
 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
 <change_format>
 <when input="output_format_images" value="png" format="png" />
 <when input="output_format_images" value="pdf" format="pdf" />
 <when input="output_format_images" value="svg" format="svg" />
 </change_format>
 </data>
-<data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
+<data format="RData" name="output_RData_obj" label="edgeR DGE on ${on_string}: R data object">
 <filter>outputs and ("make_output_RData_obj" in outputs)</filter>
 </data>
-<data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
+<data format="txt" name="output_R" label="edgeR DGE on ${on_string}: R output (debug)" >
 <filter>outputs and ("make_output_R_stdout" in outputs)</filter>
 </data>
 </outputs>
 <tests>
 <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="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" />
-<param name="output_format_images" value="png" />
+<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>
+<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="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="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.batch-effects.txt" />
+<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.batch-effects.tabular.txt" />
 </test>
 </tests>
 <help>
 edgeR: Differential Gene(Expression) Analysis
 - Tumor-Normal
 - African-European
 - 0.5*(Control+Placebo) / Treated
-Installation
-------------
-This tool requires no specific configuration. The following dependencies will installed automatically:
-- R
-- limma
-- edgeR
-License
--------
-- R
-- GPL 2 &amp; GPL 3
-- limma
-- GPL (&gt;=2)
-- edgeR
-- GPL (&gt;=2)
 @CONTACT@
 </help>
 <expand macro="citations" />
 </tool>

Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 5:bde663b872d9 draft