Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Differential_Gene_Expression.xml @ 113:f871dff92e7c draft

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author yhoogstrate
date Tue, 01 Sep 2015 07:41:17 -0400
parents b9abc9d3b429
children 5d7efbca6c75
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
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3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
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5 <macros>
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6 <import>edgeR_macros.xml</import>
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7 </macros>
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8
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9 <requirements>
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10 <requirement type="package" version="3.11.0">edger</requirement>
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11 </requirements>
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13 <stdio>
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14 <regex match="Error in[^a-z]+contrasts"
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15 source="both"
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16 level="fatal"
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17 description="Have the design- and expression-matrix been swapped?" />
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18 <regex match="Execution halted"
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19 source="both"
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20 level="fatal" />
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21 <regex match="Calculating library sizes from column"
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22 source="stderr"
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23 level="log" />
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24 <regex match="During startup - Warning messages"
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25 source="stderr"
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26 level="log" />
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27 <regex match="Setting LC_[^ ]+ failed"
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28 source="stderr"
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29 level="warning"
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30 description="LOCALE has not been set correctly" />
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31 </stdio>
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32
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33 <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>
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35 <command>
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36 R --vanilla --slave -f $R_script '--args
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37 $expression_matrix
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38 $design_matrix
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39 $contrast
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41 $fdr
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43 $output_count_edgeR
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44 $output_cpm
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46 /dev/null <!-- Calculation of FPKM/RPKM should come here -->
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48 #if $output_raw_counts:
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49 $output_raw_counts
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50 #else:
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51 /dev/null
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52 #end if
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54 #if $output_MDSplot_logFC:
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55 $output_MDSplot_logFC
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56 #else:
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57 /dev/null
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58 #end if
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60 #if $output_MDSplot_bcv:
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61 $output_MDSplot_bcv
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62 #else:
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63 /dev/null
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64 #end if
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65
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66 #if $output_BCVplot:
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67 $output_BCVplot
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68 #else:
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69 /dev/null
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70 #end if
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72 #if $output_MAplot:
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73 $output_MAplot
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74 #else:
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75 /dev/null
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76 #end if
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78 #if $output_PValue_distribution_plot:
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79 $output_PValue_distribution_plot
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80 #else:
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81 /dev/null
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82 #end if
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83
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84 #if $output_hierarchical_clustering_plot:
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85 $output_hierarchical_clustering_plot
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86 #else:
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87 /dev/null
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88 #end if
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89
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90 #if $output_heatmap_plot:
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91 $output_heatmap_plot
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92 #else:
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93 /dev/null
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94 #end if
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95
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96 #if $output_RData_obj:
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97 $output_RData_obj
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98 #else:
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99 /dev/null
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100 #end if
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101
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102 $output_format_images
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103 '
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104 #if $output_R:
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105 > $output_R
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106 #else:
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107 > /dev/null
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108 #end if
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109 </command>
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110
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111 <configfiles>
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112 <configfile name="R_script">
107
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113 <![CDATA[
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114
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115 library(limma,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
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116 library(edgeR,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
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117 library(splines,quietly=TRUE)## quietly to avoid unnecessaity stderr messages
105
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118
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119 ## Fetch commandline arguments
107
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120 args <- commandArgs(trailingOnly = TRUE)
105
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121
107
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122 expression_matrix_file <- args[1]
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123 design_matrix_file <- args[2]
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124 contrast <- args[3]
105
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125
107
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126 fdr <- args[4]
105
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127
107
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128 output_count_edgeR <- args[5]
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129 output_cpm <- args[6]
105
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130
107
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131 output_xpkm <- args[7] ##FPKM file - to be implemented
105
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132
107
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133 output_raw_counts <- args[8]
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134 output_MDSplot_logFC <- args[9]
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135 output_MDSplot_bcv <- args[10]
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136 output_BCVplot <- args[11]
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137 output_MAplot <- args[12]
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138 output_PValue_distribution_plot <- args[13]
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139 output_hierarchical_clustering_plot <- args[14]
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140 output_heatmap_plot <- args[15]
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141 output_RData_obj <- args[16]
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142 output_format_images <- args[17]
105
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143
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144
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145 ## Obtain read-counts
107
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146 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
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147 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
105
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148
107
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149 colnames(design_matrix) <- make.names(colnames(design_matrix))
105
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150
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151 for(i in 1:ncol(design_matrix)) {
107
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152 old <- design_matrix[,i]
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153 design_matrix[,i] <- make.names(design_matrix[,i])
105
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154 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
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155 print("Renaming of factors:")
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156 print(old)
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157 print("To:")
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158 print(design_matrix[,i])
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159 }
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160 ## The following line seems to malfunction the script:
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161 ##design_matrix[,i] <- as.factor(design_matrix[,i])
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162 }
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163
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164 ## 1) In the expression matrix, you only want to have the samples described in the design matrix
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165 columns <- match(rownames(design_matrix),colnames(expression_matrix))
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166 columns <- columns[!is.na(columns)]
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167 read_counts <- expression_matrix[,columns]
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168
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169 ## 2) In the design matrix, you only want to have samples of which you really have the counts
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170 columns <- match(colnames(read_counts),rownames(design_matrix))
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171 columns <- columns[!is.na(columns)]
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172 design_matrix <- design_matrix[columns,,drop=FALSE]
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173
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174 ## Filter for HTSeq predifined counts:
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175 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
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176 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
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177
107
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178 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq),rownames(read_counts))
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179 exclude <- exclude[is.na(exclude)==0]
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180 if(length(exclude) != 0) {
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181 read_counts <- read_counts[-exclude,]
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182 }
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183
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184
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185 ## sorting expression matrix with the order of the read_counts
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186 ##order <- match(colnames(read_counts) , rownames(design_matrix))
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187 ##read_counts_ordered <- read_counts[,order2]
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188
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189 empty_samples <- apply(read_counts,2,function(x) sum(x) == 0)
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190 if(sum(empty_samples) > 0) {
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191 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr())
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192 write(colnames(read_counts)[empty_samples],stderr())
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193 } else {
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194
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195 dge <- DGEList(counts=read_counts,genes=rownames(read_counts))
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196
107
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197 formula <- paste(c("~0",make.names(colnames(design_matrix))),collapse = " + ")
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198 design_matrix_tmp <- design_matrix
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199 colnames(design_matrix_tmp) <- make.names(colnames(design_matrix_tmp))
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200 design <- model.matrix(as.formula(formula),design_matrix_tmp)
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201 rm(design_matrix_tmp)
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202
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203 # Filter prefixes
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204 prefixes = colnames(design_matrix)[attr(design,"assign")]
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205 avoid = nchar(prefixes) == nchar(colnames(design))
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206 replacements = substr(colnames(design),nchar(prefixes)+1,nchar(colnames(design)))
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207 replacements[avoid] = colnames(design)[avoid]
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208 colnames(design) = replacements
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209
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210 # Do normalization
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211 write("Calculating normalization factors...",stdout())
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212 dge <- calcNormFactors(dge)
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213 write("Estimating common dispersion...",stdout())
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214 dge <- estimateGLMCommonDisp(dge,design)
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215 write("Estimating trended dispersion...",stdout())
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216 dge <- estimateGLMTrendedDisp(dge,design)
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217 write("Estimating tagwise dispersion...",stdout())
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218 dge <- estimateGLMTagwiseDisp(dge,design)
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219
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220
111
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221 # hierarchical clustering makes use of the distance of the MDS
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222 if(output_MDSplot_logFC != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
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223 write("Calculating MDS plot (logFC method)",stdout())
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224 mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)))# Get coordinates of unflexible plot
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225 dev.off()# Kill it
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226
111
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227 if(output_MDSplot_logFC != "/dev/null") {
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228 write("Creating MDS plot (logFC method)",stdout())
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229 if(output_format_images == "pdf") {
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230 pdf(output_MDSplot_logFC,height=14,width=14)
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231 } else if(output_format_images == "svg") {
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232 svg(output_MDSplot_logFC,height=14,width=14)
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233 } else {
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234 ## png(output_MDSplot_logFC)
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235 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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236
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237 bitmap(output_MDSplot_logFC,type="png16m",height=7*3,width=7*3)
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238 }
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239
111
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240 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
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241 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
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242 plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
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243 mds_distance_logFC(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
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244 text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
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245 rm(diff_x,diff_y)
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246
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247 dev.off()
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248 }
105
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249 }
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250
111
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251
105
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252 if(output_MDSplot_bcv != "/dev/null") {
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253 write("Creating MDS plot (bcv method)",stdout())
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254
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255 ## 1. First create a virtual plot to obtain the desired coordinates
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256 pdf("bcvmds.pdf")
111
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257 mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)))
105
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258 dev.off()# Kill it
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259
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260 ## 2. Re-plot the coordinates in a new figure with the size and settings.
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261 if(output_format_images == "pdf") {
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262 pdf(output_MDSplot_bcv,height=14,width=14)
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263 } else if(output_format_images == "svg") {
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264 svg(output_MDSplot_bcv,height=14,width=14)
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265 } else {
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266 ## png(output_MDSplot_bcv)
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267 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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268
111
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269 bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3)
105
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270 }
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271
111
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272 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
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273 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
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274 plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
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275 mds_distance_BCV(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
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276 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
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277 rm(diff_x,diff_y)
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278
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279 dev.off()
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280 }
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281
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282
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283 if(output_BCVplot != "/dev/null") {
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284 write("Creating Biological coefficient of variation plot",stdout())
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285
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286 if(output_format_images == "pdf") {
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287 pdf(output_BCVplot)
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288 } else if(output_format_images == "svg") {
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289 svg(output_BCVplot)
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290 } else {
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291 ## png(output_BCVplot)
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292 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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293
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294 bitmap(output_BCVplot,type="png16m",width=10.5*3,height=7*3)
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295 }
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296
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297 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
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298 dev.off()
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299 }
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300
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301
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302 write("Fitting GLM...",stdout())
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303 fit <- glmFit(dge,design)
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304
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305 write(paste("Performing likelihood ratio test: ",contrast,sep=""),stdout())
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306 cont <- c(contrast)
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307 cont <- makeContrasts(contrasts=cont, levels=design)
105
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308
107
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309 lrt <- glmLRT(fit, contrast=cont[,1])
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310 write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
105
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311 write.table(file=output_count_edgeR,topTags(lrt,n=nrow(read_counts))\$table,sep="\t",row.names=TRUE,col.names=NA)
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312 write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA)
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313
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314 ## todo EXPORT FPKM
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315 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
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316
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317 if(output_MAplot != "/dev/null" || output_PValue_distribution_plot != "/dev/null") {
107
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318 etable <- topTags(lrt, n=nrow(dge))\$table
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319 etable <- etable[order(etable\$FDR), ]
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320
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321 if(output_MAplot != "/dev/null") {
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322 write("Creating MA plot...",stdout())
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323
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324 if(output_format_images == "pdf") {
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325 pdf(output_MAplot)
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326 } else if(output_format_images == "svg") {
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327 svg(output_MAplot)
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328 } else {
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329 ## png(output_MAplot)
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330 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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331
111
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332 bitmap(output_MAplot,type="png16m",width=10.5*3,height=7*3)
105
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333 }
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334
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335 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
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336 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
105
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337 abline(h=c(-1,1), col="blue")
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338 dev.off()
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339 }
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340
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341 if(output_PValue_distribution_plot != "/dev/null") {
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342 write("Creating P-value distribution plot...",stdout())
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343
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344 if(output_format_images == "pdf") {
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345 pdf(output_PValue_distribution_plot,width=14,height=14)
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346 } else if(output_format_images == "svg") {
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347 svg(output_PValue_distribution_plot,width=14,height=14)
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348 } else {
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349 ## png(output_PValue_distribution_plot)
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350 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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351
111
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352 bitmap(output_PValue_distribution_plot,type="png16m",width=7*3,height=7*3)
105
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353 }
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354
109
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355 expressed_genes <- subset(etable, PValue < 0.99)
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356 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
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357 center <- sum(h\$counts) / length(h\$counts)
105
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358 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2)
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359 k <- ksmooth(h\$mid, h\$counts)
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360 lines(k\$x,k\$y,col="red",lwd=2)
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361 rmsd <- (h\$counts) - center
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362 rmsd <- rmsd^2
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363 rmsd <- sum(rmsd)
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364 rmsd <- sqrt(rmsd)
105
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365 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue")
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366 ## change e into epsilon somehow
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367 dev.off()
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368 }
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369 }
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370
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371 if(output_heatmap_plot != "/dev/null") {
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372
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373 if(output_format_images == "pdf") {
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374 pdf(output_heatmap_plot,width=10.5)
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375 } else if(output_format_images == "svg") {
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376 svg(output_heatmap_plot,width=10.5)
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377 } else {
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378 ## png(output_heatmap_plot)
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379 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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380
111
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381 bitmap(output_heatmap_plot,type="png16m",width=10.5*3,height=7*3)
105
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382 }
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383
107
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384 etable2 <- topTags(lrt, n=100)\$table
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385 order <- rownames(etable2)
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386 cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
105
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387 heatmap(t(cpm_sub))
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388 dev.off()
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389 }
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390
111
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391 if(output_hierarchical_clustering_plot != "/dev/null") {
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392 if(output_hierarchical_clustering_plot == "pdf") {
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393 pdf(output_hierarchical_clustering_plot,width=10.5)
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394 } else if(output_hierarchical_clustering_plot == "svg") {
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395 svg(output_hierarchical_clustering_plot,width=10.5)
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396 } else {
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397 ## png(output_hierarchical_clustering_plot)
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398 ## png does not work out of the box in the Galaxy Toolshed Version of R due to its compile settings: https://biostar.usegalaxy.org/p/9170/
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399
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400 bitmap(output_hierarchical_clustering_plot,type="png16m",width=10.5*3,height=7*3)
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401 }
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402
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403 mds_distance = as.dist(mds_distance_logFC\$distance.matrix)
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404 clustering = hclust(mds_distance)
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405 plot(clustering,main=paste("Cluster Dendogram on the ",mds_distance_logFC\$top," TopTags",sep="",sub="\ncomplete linkage on logFC MDS distance"))
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406
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407 dev.off()
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408 }
105
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409
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410 if(output_RData_obj != "/dev/null") {
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411 save.image(output_RData_obj)
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412 }
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413
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414 write("Done!",stdout())
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415 }
107
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416 ]]>
105
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417 </configfile>
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418 </configfiles>
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419
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420 <inputs>
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421 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" />
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422 <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'." />
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423
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424 <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." />
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425
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426 <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" />
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427
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428 <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes">
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429 <option value="make_output_raw_counts">Raw counts table</option>
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430 <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option>
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431 <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; much slower)</option>
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432 <option value="make_output_BCVplot">BCV-plot</option>
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433 <option value="make_output_MAplot">MA-plot</option>
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434 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
111
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435 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
105
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436 <option value="make_output_heatmap_plot">Heatmap</option>
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437
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438 <option value="make_output_R_stdout">R stdout</option>
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439 <option value="make_output_RData_obj">R Data object</option>
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440 </param>
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441
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442 <param name="output_format_images" type="select" label="Output format of images" display="radio">
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443 <option value="png">Portable network graphics (.png)</option>
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444 <option value="pdf">Portable document format (.pdf)</option>
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445 <option value="svg">Scalable vector graphics (.svg)</option>
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446 </param>
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447 </inputs>
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448
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449 <outputs>
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450 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
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451 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
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452
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453 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
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454 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
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455 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
456
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
457 <data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (logFC method)">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
458 <filter>outputs and ("make_output_MDSplot_logFC" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
459
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
460 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
461 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
462 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
463 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
464 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
465 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
466
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
467 <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
468 <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
469
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
470 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
471 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
472 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
473 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
474 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
475 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
476
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
477 <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
478 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
479
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
480 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
481 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
482 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
483 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
484 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
485 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
486
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
487 <data format="png" name="output_MAplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MA-plot">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
488 <filter>outputs and ("make_output_MAplot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
489
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
490 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
491 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
492 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
493 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
494 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
495 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
496
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
497 <data format="png" name="output_PValue_distribution_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - P-Value distribution">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
498 <filter>outputs and ("make_output_PValue_distribution_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
499
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
500 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
501 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
502 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
503 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
504 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
505 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
506
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
507 <data format="png" name="output_hierarchical_clustering_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Hierarchical custering">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
508 <filter>outputs and ("make_output_hierarchical_clustering_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
509
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
510 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
511 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
512 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
513 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
514 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
515 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
516
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
517 <data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
518 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
519
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
520 <change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
521 <when input="output_format_images" value="png" format="png" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
522 <when input="output_format_images" value="pdf" format="pdf" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
523 <when input="output_format_images" value="svg" format="svg" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
524 </change_format>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
525 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
526
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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diff changeset
527 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object">
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
528 <filter>outputs and ("make_output_RData_obj" in outputs)</filter>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
diff changeset
529 </data>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
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530
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531 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" >
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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532 <filter>outputs and ("make_output_R_stdout" in outputs)</filter>
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533 </data>
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534 </outputs>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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535
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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536 <tests>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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537 <test>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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538 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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539 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" />
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540
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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541 <param name="contrast" value="E-C"/>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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542
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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543 <param name="fdr" value="0.05" />
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544
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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545 <param name="output_format_images" value="png" />
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546
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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547 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" />
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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548 </test>
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549 </tests>
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550
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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551 <help>
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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552 edgeR: Differential Gene(Expression) Analysis
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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553 #############################################
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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554
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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555 Overview
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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556 --------
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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557 Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication. Uses empirical Bayes estimation and exact tests based on the negative binomial distribution. Also useful for differential signal analysis with other types of genome-scale count data [1].
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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558
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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559 For every experiment, the algorithm requires a design matrix. This matrix describes which samples belong to which groups.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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560 More details on this are given in the edgeR manual: http://www.bioconductor.org/packages/2.12/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
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561 and the limma manual.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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562
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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563 Because the creation of a design matrix can be complex and time consuming, especially if no GUI is used, this package comes with an alternative tool which can help you with it.
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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564 This tool is called *edgeR Design Matrix Creator*.
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565 If the appropriate design matrix (with corresponding links to the files) is given,
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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566 the correct contrast ( http://en.wikipedia.org/wiki/Contrast_(statistics) ) has to be given.
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567
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568 If you have for example two groups, with an equal weight, you would like to compare either
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569 "g1-g2" or "normal-cancer".
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570
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571 The test function makes use of a MCF7 dataset used in a study that indicates that a higher sequencing depth is not neccesairily more important than a higher amount of replaciates[2].
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572
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573 Input
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574 -----
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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575 Expression matrix
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576 ^^^^^^^^^^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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577 ::
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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578
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579 Geneid "\t" Sample-1 "\t" Sample-2 "\t" Sample-3 "\t" Sample-4 [...] "\n"
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580 SMURF "\t" 123 "\t" 21 "\t" 34545 "\t" 98 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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581 BRCA1 "\t" 435 "\t" 6655 "\t" 45 "\t" 55 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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582 LINK33 "\t" 4 "\t" 645 "\t" 345 "\t" 1 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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583 SNORD78 "\t" 498 "\t" 65 "\t" 98 "\t" 27 ... "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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584 [...]
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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585
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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586 *Note: Make sure the number of columns in the header is identical to the number of columns in the body.*
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587
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588 Design matrix
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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589 ^^^^^^^^^^^^^
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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590 ::
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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591
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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592 Sample "\t" Condition "\t" Ethnicity "\t" Patient "\t" Batch "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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593 Sample-1 "\t" Tumor "\t" European "\t" 1 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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594 Sample-2 "\t" Normal "\t" European "\t" 1 "\t" 1 "\n"
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595 Sample-3 "\t" Tumor "\t" European "\t" 2 "\t" 1 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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596 Sample-4 "\t" Normal "\t" European "\t" 2 "\t" 1 "\n"
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597 Sample-5 "\t" Tumor "\t" African "\t" 3 "\t" 1 "\n"
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598 Sample-6 "\t" Normal "\t" African "\t" 3 "\t" 1 "\n"
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599 Sample-7 "\t" Tumor "\t" African "\t" 4 "\t" 2 "\n"
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600 Sample-8 "\t" Normal "\t" African "\t" 4 "\t" 2 "\n"
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601 Sample-9 "\t" Tumor "\t" Asian "\t" 5 "\t" 2 "\n"
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602 Sample-10 "\t" Normal "\t" Asian "\t" 5 "\t" 2 "\n"
f2ac9f6bc542 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
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603 Sample-11 "\t" Tumor "\t" Asian "\t" 6 "\t" 2 "\n"
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604 Sample-12 "\t" Normal "\t" Asian "\t" 6 "\t" 2 "\n"
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605
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606 *Note: Avoid factor names that are (1) numerical, (2) contain mathematical symbols and preferebly only use letters.*
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607
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608 Contrast
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609 ^^^^^^^^
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610 The contrast represents the biological question. There can be many questions asked, e.g.:
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611
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612 - Tumor-Normal
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613 - African-European
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614 - 0.5*(Control+Placebo) / Treated
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615
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616 Installation
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617 ------------
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618
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619 This tool requires no specific configurations. The following dependencies are installed automatically:
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620
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621 - R
108
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622 - limma
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623 - edgeR
105
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624
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625 License
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626 -------
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627 - R
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628 - GPL 2 &amp; GPL 3
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629 - limma
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630 - GPL (&gt;=2)
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631 - edgeR
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632 - GPL (&gt;=2)
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633
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634 References
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635 ----------
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636
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637 EdgeR
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638 ^^^^^
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639 **[1] edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.**
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640
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641 *Mark D. Robinson, Davis J. McCarthy and Gordon K. Smyth* - Bioinformatics (2010) 26 (1): 139-140.
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642
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643 - http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html
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644 - http://dx.doi.org/10.1093/bioinformatics/btp616
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645 - http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
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646
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647 Test-data (MCF7)
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648 ^^^^^^^^^^^^^^^^
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649 **[2] RNA-seq differential expression studies: more sequence or more replication?**
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650
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651 *Yuwen Liu, Jie Zhou and Kevin P. White* - Bioinformatics (2014) 30 (3): 301-304.
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652
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653 - http://www.ncbi.nlm.nih.gov/pubmed/24319002
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654 - http://dx.doi.org/10.1093/bioinformatics/btt688
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655
108
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656 @CONTACT@
105
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657 </help>
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658
108
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659 <expand macro="citations" />
105
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660 </tool>