annotate edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft

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author yhoogstrate
date Wed, 09 Dec 2015 10:42:33 -0500
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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.b">
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3 <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
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4
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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="Error in eval\(expr, envir, enclos\)"
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19 source="both"
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20 level="fatal"
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21 description="You have most likely used a condition in the contrast, that is not present in the Design matrix" />
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22 <regex match="Execution halted"
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23 source="both"
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24 level="fatal" />
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25 <regex match="Calculating library sizes from column"
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26 source="stderr"
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27 level="log" />
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28 <regex match="During startup - Warning messages"
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29 source="stderr"
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30 level="log" />
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31 <regex match="Setting LC_[^ ]+ failed"
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32 source="stderr"
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33 level="warning"
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34 description="LOCALE has not been set correctly" />
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35 </stdio>
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36
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37 <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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39 <command>
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40 R --vanilla --slave -f $R_script '--args
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41 $expression_matrix
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42 $design_matrix
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43 $contrast
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44
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45 $fdr
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46
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47 $output_count_edgeR
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48 $output_cpm
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49
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50 /dev/null <!-- Calculation of FPKM/RPKM should come here -->
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52 #if $output_raw_counts:
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53 $output_raw_counts
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54 #else:
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55 /dev/null
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56 #end if
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57
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58 #if $output_MDSplot_logFC:
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59 $output_MDSplot_logFC
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60 #else:
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61 /dev/null
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62 #end if
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63
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64 #if $output_MDSplot_logFC_coordinates:
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65 $output_MDSplot_logFC_coordinates
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66 #else:
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67 /dev/null
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68 #end if
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69
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70 #if $output_MDSplot_bcv:
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71 $output_MDSplot_bcv
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72 #else:
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73 /dev/null
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74 #end if
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75
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76 #if $output_MDSplot_bcv_coordinates:
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77 $output_MDSplot_bcv_coordinates
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78 #else:
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79 /dev/null
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80 #end if
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81
105
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82 #if $output_BCVplot:
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83 $output_BCVplot
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84 #else:
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85 /dev/null
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86 #end if
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87
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88 #if $output_MAplot:
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89 $output_MAplot
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90 #else:
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91 /dev/null
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92 #end if
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93
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94 #if $output_PValue_distribution_plot:
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95 $output_PValue_distribution_plot
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96 #else:
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97 /dev/null
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98 #end if
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99
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100 #if $output_hierarchical_clustering_plot:
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101 $output_hierarchical_clustering_plot
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102 #else:
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103 /dev/null
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104 #end if
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105
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106 #if $output_heatmap_plot:
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107 $output_heatmap_plot
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108 #else:
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109 /dev/null
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110 #end if
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111
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112 #if $output_RData_obj:
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113 $output_RData_obj
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114 #else:
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115 /dev/null
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116 #end if
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117
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118 $output_format_images
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119 '
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120 </command>
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121
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122 <configfiles>
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123 <configfile name="R_script">
107
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124 <![CDATA[
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125
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126 library(limma,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
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127 library(edgeR,quietly=TRUE) ## quietly to avoid unnecessaity stderr messages
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128 library(splines,quietly=TRUE)## quietly to avoid unnecessaity stderr messages
105
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129
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130 ## Fetch commandline arguments
107
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131 args <- commandArgs(trailingOnly = TRUE)
105
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132
107
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133 expression_matrix_file <- args[1]
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134 design_matrix_file <- args[2]
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135 contrast <- args[3]
105
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136
107
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137 fdr <- args[4]
105
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138
107
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139 output_count_edgeR <- args[5]
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140 output_cpm <- args[6]
105
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141
107
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142 output_xpkm <- args[7] ##FPKM file - to be implemented
105
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143
107
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144 output_raw_counts <- args[8]
117
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145
107
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146 output_MDSplot_logFC <- args[9]
117
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147 output_MDSplot_logFC_coordinates <- args[10]
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148
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149 output_MDSplot_bcv <- args[11]
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150 output_MDSplot_bcv_coordinates <- args[12]
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151
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152 output_BCVplot <- args[13]
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153 output_MAplot <- args[14]
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154 output_PValue_distribution_plot <- args[15]
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155 output_hierarchical_clustering_plot <- args[16]
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156 output_heatmap_plot <- args[17]
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157 output_RData_obj <- args[18]
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158 output_format_images <- args[19]
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159
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160
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161 ## Obtain read-counts
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162 expression_matrix <- read.delim(expression_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
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163 design_matrix <- read.delim(design_matrix_file,header=T,stringsAsFactors=F,row.names=1,check.names=FALSE,na.strings=c(""))
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164
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165 colnames(design_matrix) <- make.names(colnames(design_matrix))
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166
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167 for(i in 1:ncol(design_matrix)) {
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168 old <- design_matrix[,i]
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169 design_matrix[,i] <- make.names(design_matrix[,i])
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170 if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
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171 print("Renaming of factors:")
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172 print(old)
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173 print("To:")
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174 print(design_matrix[,i])
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175 }
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176 ## The following line seems to malfunction the script:
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177 ##design_matrix[,i] <- as.factor(design_matrix[,i])
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178 }
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179
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180 ## 1) In the expression matrix, you only want to have the samples described in the design matrix
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181 columns <- match(rownames(design_matrix),colnames(expression_matrix))
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182 columns <- columns[!is.na(columns)]
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183 read_counts <- expression_matrix[,columns]
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184
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185 ## 2) In the design matrix, you only want to have samples of which you really have the counts
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186 columns <- match(colnames(read_counts),rownames(design_matrix))
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187 columns <- columns[!is.na(columns)]
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188 design_matrix <- design_matrix[columns,,drop=FALSE]
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189
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190 ## Filter for HTSeq predifined counts:
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191 exclude_HTSeq <- c("no_feature","ambiguous","too_low_aQual","not_aligned","alignment_not_unique")
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192 exclude_DEXSeq <- c("_ambiguous","_empty","_lowaqual","_notaligned")
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193 exclude_STAR <- c("N_unmapped", "N_multimapping", "N_noFeature", "N_ambiguous")
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194
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195 exclude <- match(c(exclude_HTSeq, exclude_DEXSeq, exclude_STAR),rownames(read_counts))
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196 exclude <- exclude[is.na(exclude)==0]
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197 if(length(exclude) != 0) {
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198 read_counts <- read_counts[-exclude,]
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199 }
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200
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201
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202 ## sorting expression matrix with the order of the read_counts
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203 ##order <- match(colnames(read_counts) , rownames(design_matrix))
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204 ##read_counts_ordered <- read_counts[,order2]
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205
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206 empty_samples <- apply(read_counts,2,function(x) sum(x) == 0)
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207 if(sum(empty_samples) > 0) {
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208 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr())
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209 write(colnames(read_counts)[empty_samples],stderr())
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210 } else {
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211
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212 dge <- DGEList(counts=read_counts,genes=rownames(read_counts))
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213
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214 formula <- paste(c("~0",make.names(colnames(design_matrix))),collapse = " + ")
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215 design_matrix_tmp <- design_matrix
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216 colnames(design_matrix_tmp) <- make.names(colnames(design_matrix_tmp))
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217 design <- model.matrix(as.formula(formula),design_matrix_tmp)
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218 rm(design_matrix_tmp)
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219
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220 # Filter prefixes
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221 prefixes = colnames(design_matrix)[attr(design,"assign")]
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222 avoid = nchar(prefixes) == nchar(colnames(design))
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223 replacements = substr(colnames(design),nchar(prefixes)+1,nchar(colnames(design)))
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224 replacements[avoid] = colnames(design)[avoid]
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225 colnames(design) = replacements
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226
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227 # Do normalization
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228 write("Calculating normalization factors...",stdout())
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229 dge <- calcNormFactors(dge)
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230 write("Estimating common dispersion...",stdout())
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231 dge <- estimateGLMCommonDisp(dge,design)
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232 write("Estimating trended dispersion...",stdout())
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233 dge <- estimateGLMTrendedDisp(dge,design)
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234 write("Estimating tagwise dispersion...",stdout())
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235 dge <- estimateGLMTagwiseDisp(dge,design)
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236
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237
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238 # hierarchical clustering makes use of the distance of the MDS
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239 if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
111
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240 write("Calculating MDS plot (logFC method)",stdout())
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241 n_dim <- nrow(dge\$samples)
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242 mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
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243 dev.off()# Kill it
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244
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245 # Reset to primary dimensions
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246 mds_distance_logFC\$x = mds_distance_logFC\$cmdscale.out[,1]
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247 mds_distance_logFC\$y = mds_distance_logFC\$cmdscale.out[,2]
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248
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249 if(output_MDSplot_logFC != "/dev/null") {
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250 write("Creating MDS plot (logFC method)",stdout())
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251 if(output_format_images == "pdf") {
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252 pdf(output_MDSplot_logFC,height=14,width=14)
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253 } else if(output_format_images == "svg") {
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254 svg(output_MDSplot_logFC,height=14,width=14)
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255 } else {
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256 ## png(output_MDSplot_logFC)
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257 ## 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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258
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259 bitmap(output_MDSplot_logFC,type="png16m",height=7*3,width=7*3)
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260 }
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261
111
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262 diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
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263 diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
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264 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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265 points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
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266 text(mds_distance_logFC\$x,mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
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267 rm(diff_x,diff_y)
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268
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269 dev.off()
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270 }
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271
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272 if(output_MDSplot_logFC_coordinates != "/dev/null") {
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273 n_dim <- ncol(mds_distance_logFC\$cmdscale.out)
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274 colnames(mds_distance_logFC\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
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275 export <- data.frame(samples=rownames(mds_distance_logFC\$cmdscale.out),mds_distance_logFC\$cmdscale.out)
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276 row.names(export) <- NULL
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277 write.table(file=output_MDSplot_logFC_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
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278 }
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279 }
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280
111
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281
117
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282 if(output_MDSplot_bcv != "/dev/null" || output_MDSplot_bcv_coordinates != "/dev/null" ) {
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283 write("Creating MDS plot (bcv method)",stdout())
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284
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285 ## 1. First create a virtual plot to obtain the desired coordinates
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286 n_dim <- nrow(dge\$samples)
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287 mds_distance_BCV <- plotMDS.DGEList(dge,method="bcv",top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
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288 dev.off()
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289
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290 if(output_MDSplot_logFC != "/dev/null") {
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291 ## 2. Re-plot the coordinates in a new figure with the size and settings.
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292 if(output_format_images == "pdf") {
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293 pdf(output_MDSplot_bcv,height=14,width=14)
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294 } else if(output_format_images == "svg") {
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295 svg(output_MDSplot_bcv,height=14,width=14)
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296 } else {
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297 ## png(output_MDSplot_bcv)
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298 ## 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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299
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300 bitmap(output_MDSplot_bcv,type="png16m",height=7*3,width=7*3)
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301 }
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302
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303 diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
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304 diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
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305 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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306 points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
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307 text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
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308 rm(diff_x,diff_y)
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309
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310 dev.off()
105
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311 }
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312
117
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313 if(output_MDSplot_bcv_coordinates != "/dev/null") {
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314 n_dim <- ncol(mds_distance_BCV\$cmdscale.out)
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315 colnames(mds_distance_BCV\$cmdscale.out) <- paste(rep("Dim",n_dim),(1:n_dim),sep="_")
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316 export <- data.frame(samples=rownames(mds_distance_BCV\$cmdscale.out),mds_distance_BCV\$cmdscale.out)
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317 row.names(export) <- NULL
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318 write.table(file=output_MDSplot_bcv_coordinates,export,sep="\t",row.names=FALSE,col.names=TRUE)
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319 }
105
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320 }
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321
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322
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323 if(output_BCVplot != "/dev/null") {
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324 write("Creating Biological coefficient of variation plot",stdout())
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325
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326 if(output_format_images == "pdf") {
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327 pdf(output_BCVplot)
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328 } else if(output_format_images == "svg") {
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329 svg(output_BCVplot)
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330 } else {
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331 ## png(output_BCVplot)
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332 ## 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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333
111
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334 bitmap(output_BCVplot,type="png16m",width=10.5*3,height=7*3)
105
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335 }
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336
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337 plotBCV(dge, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")
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338 dev.off()
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339 }
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340
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341
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342 write("Fitting GLM...",stdout())
107
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343 fit <- glmFit(dge,design)
105
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344
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345 write(paste("Performing likelihood ratio test: ",contrast,sep=""),stdout())
107
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346 cont <- c(contrast)
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347 cont <- makeContrasts(contrasts=cont, levels=design)
105
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348
107
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349 lrt <- glmLRT(fit, contrast=cont[,1])
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350 write(paste("Exporting DGE results to file...",output_count_edgeR,sep=""),stdout())
105
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351 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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352 write.table(file=output_cpm,cpm(dge,normalized.lib.sizes=TRUE),sep="\t",row.names=TRUE,col.names=NA)
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353
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354 ## todo EXPORT FPKM
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355 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
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356
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357 if(output_MAplot != "/dev/null" || output_PValue_distribution_plot != "/dev/null") {
107
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358 etable <- topTags(lrt, n=nrow(dge))\$table
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359 etable <- etable[order(etable\$FDR), ]
105
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360
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361 if(output_MAplot != "/dev/null") {
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362 write("Creating MA plot...",stdout())
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363
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364 if(output_format_images == "pdf") {
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365 pdf(output_MAplot)
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366 } else if(output_format_images == "svg") {
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367 svg(output_MAplot)
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368 } else {
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369 ## png(output_MAplot)
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370 ## 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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371
111
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372 bitmap(output_MAplot,type="png16m",width=10.5*3,height=7*3)
105
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373 }
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374
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375 with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
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376 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
105
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377 abline(h=c(-1,1), col="blue")
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378 dev.off()
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379 }
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380
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381 if(output_PValue_distribution_plot != "/dev/null") {
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382 write("Creating P-value distribution plot...",stdout())
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383
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384 if(output_format_images == "pdf") {
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385 pdf(output_PValue_distribution_plot,width=14,height=14)
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386 } else if(output_format_images == "svg") {
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387 svg(output_PValue_distribution_plot,width=14,height=14)
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388 } else {
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389 ## png(output_PValue_distribution_plot)
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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390 ## 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/
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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391
111
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392 bitmap(output_PValue_distribution_plot,type="png16m",width=7*3,height=7*3)
105
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393 }
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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394
109
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395 expressed_genes <- subset(etable, PValue < 0.99)
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396 h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
107
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397 center <- sum(h\$counts) / length(h\$counts)
105
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398 lines(c(0,1),c(center,center),lty=2,col="red",lwd=2)
107
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399 k <- ksmooth(h\$mid, h\$counts)
105
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400 lines(k\$x,k\$y,col="red",lwd=2)
107
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401 rmsd <- (h\$counts) - center
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402 rmsd <- rmsd^2
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403 rmsd <- sum(rmsd)
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404 rmsd <- sqrt(rmsd)
105
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405 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue")
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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406 ## change e into epsilon somehow
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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407 dev.off()
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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408 }
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409 }
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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410
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411 if(output_heatmap_plot != "/dev/null") {
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412
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413 if(output_format_images == "pdf") {
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414 pdf(output_heatmap_plot,width=10.5)
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415 } else if(output_format_images == "svg") {
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416 svg(output_heatmap_plot,width=10.5)
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417 } else {
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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418 ## png(output_heatmap_plot)
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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419 ## 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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420
111
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421 bitmap(output_heatmap_plot,type="png16m",width=10.5*3,height=7*3)
105
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422 }
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423
107
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424 etable2 <- topTags(lrt, n=100)\$table
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425 order <- rownames(etable2)
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426 cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),]
105
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427 heatmap(t(cpm_sub))
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428 dev.off()
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429 }
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430
111
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431 if(output_hierarchical_clustering_plot != "/dev/null") {
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432 if(output_hierarchical_clustering_plot == "pdf") {
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433 pdf(output_hierarchical_clustering_plot,width=10.5)
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434 } else if(output_hierarchical_clustering_plot == "svg") {
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435 svg(output_hierarchical_clustering_plot,width=10.5)
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436 } else {
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689
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437 ## png(output_hierarchical_clustering_plot)
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438 ## 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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439
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440 bitmap(output_hierarchical_clustering_plot,type="png16m",width=10.5*3,height=7*3)
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441 }
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689
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442
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diff changeset
443 mds_distance = as.dist(mds_distance_logFC\$distance.matrix)
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444 clustering = hclust(mds_distance)
b9abc9d3b429 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689
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diff changeset
445 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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446
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diff changeset
447 dev.off()
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448 }
105
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449
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450 if(output_RData_obj != "/dev/null") {
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451 save.image(output_RData_obj)
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452 }
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453
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454 write("Done!",stdout())
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455 }
107
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456 ]]>
105
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457 </configfile>
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458 </configfiles>
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459
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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460 <inputs>
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461 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) 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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462 <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'." />
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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463
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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464 <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." />
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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465
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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466 <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" />
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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467
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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468 <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes">
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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469 <option value="make_output_raw_counts">Raw counts table</option>
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470 <option value="make_output_MDSplot_logFC">MDS-plot (logFC-method)</option>
117
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471 <option value="make_output_MDSplot_logFC_coordinates">MDS-plot coordinates table (logFC-method)</option>
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472 <option value="make_output_MDSplot_bcv">MDS-plot (BCV-method; slow)</option>
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473 <option value="make_output_MDSplot_bcv_coordinates">MDS-plot coordinates table (BCV-method; slow)</option>
105
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474 <option value="make_output_BCVplot">BCV-plot</option>
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475 <option value="make_output_MAplot">MA-plot</option>
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476 <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
111
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477 <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
105
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478 <option value="make_output_heatmap_plot">Heatmap</option>
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479 <option value="make_output_RData_obj">R Data object</option>
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480 </param>
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481
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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482 <param name="output_format_images" type="select" label="Output format of images" display="radio">
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483 <option value="png">Portable network graphics (.png)</option>
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484 <option value="pdf">Portable document format (.pdf)</option>
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485 <option value="svg">Scalable vector graphics (.svg)</option>
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486 </param>
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487 </inputs>
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488
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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489 <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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490 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" />
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491 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" />
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492
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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493 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts">
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494 <filter>outputs and ("make_output_raw_counts" in outputs)</filter>
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495 </data>
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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496
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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497 <data format="png" name="output_MDSplot_logFC" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (logFC method)">
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498 <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
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499
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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500 <change_format>
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501 <when input="output_format_images" value="png" format="png" />
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502 <when input="output_format_images" value="pdf" format="pdf" />
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503 <when input="output_format_images" value="svg" format="svg" />
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504 </change_format>
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505 </data>
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506
117
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507 <data format="tabular" name="output_MDSplot_logFC_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (logFC method)">
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508 <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter>
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509 </data>
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510
105
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511 <data format="png" name="output_MDSplot_bcv" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot (bcv method)">
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512 <filter>outputs and ("make_output_MDSplot_bcv" in outputs)</filter>
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513
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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514 <change_format>
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515 <when input="output_format_images" value="png" format="png" />
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516 <when input="output_format_images" value="pdf" format="pdf" />
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517 <when input="output_format_images" value="svg" format="svg" />
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518 </change_format>
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519 </data>
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520
117
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521 <data format="tabular" name="output_MDSplot_bcv_coordinates" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - MDS-plot coordinates table (BCV method)">
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522 <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter>
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523 </data>
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524
105
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525 <data format="png" name="output_BCVplot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - BCV-plot">
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526 <filter>outputs and ("make_output_BCVplot" in outputs)</filter>
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527
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 <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
529 <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
530 <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
531 <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
532 </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
533 </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
534
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
535 <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
536 <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
537
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
538 <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
539 <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
540 <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
541 <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
542 </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
543 </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
544
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
545 <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
546 <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
547
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
548 <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
549 <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
550 <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
551 <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
552 </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
553 </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
554
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
555 <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
556 <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
557
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
558 <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
559 <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
560 <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
561 <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
562 </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
563 </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
564
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
565 <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
parents:
diff changeset
566 <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
parents:
diff changeset
567
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
568 <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
569 <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
570 <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
571 <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
572 </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
573 </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
574
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
575 <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
576 <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
577 </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
578
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
579 <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
yhoogstrate
parents:
diff changeset
580 <filter>outputs and ("make_output_R_stdout" 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
581 </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
582 </outputs>
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
583
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
584 <tests>
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
585 <test>
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
586 <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
yhoogstrate
parents:
diff changeset
587 <param name="design_matrix" value="Differential_Gene_Expression/design_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
yhoogstrate
parents:
diff changeset
588
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
589 <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
yhoogstrate
parents:
diff changeset
590
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
591 <param name="fdr" value="0.05" />
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
592
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
593 <param name="output_format_images" value="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
594
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
595 <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
yhoogstrate
parents:
diff changeset
596 </test>
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
597 </tests>
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
598
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
599 <help>
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
600 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
yhoogstrate
parents:
diff changeset
601 #############################################
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
602
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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603 Overview
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604 --------
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605 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].
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606
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607 For every experiment, the algorithm requires a design matrix. This matrix describes which samples belong to which groups.
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608 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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609 and the limma manual.
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610
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611 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.
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612 This tool is called *edgeR Design Matrix Creator*.
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613 If the appropriate design matrix (with corresponding links to the files) is given,
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614 the correct contrast ( http://en.wikipedia.org/wiki/Contrast_(statistics) ) has to be given.
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615
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616 If you have for example two groups, with an equal weight, you would like to compare either
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617 "g1-g2" or "normal-cancer".
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618
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619 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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620
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621 Input
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622 -----
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623 Expression matrix
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624 ^^^^^^^^^^^^^^^^^
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625 ::
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626
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627 Geneid "\t" Sample-1 "\t" Sample-2 "\t" Sample-3 "\t" Sample-4 [...] "\n"
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628 SMURF "\t" 123 "\t" 21 "\t" 34545 "\t" 98 ... "\n"
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629 BRCA1 "\t" 435 "\t" 6655 "\t" 45 "\t" 55 ... "\n"
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630 LINK33 "\t" 4 "\t" 645 "\t" 345 "\t" 1 ... "\n"
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631 SNORD78 "\t" 498 "\t" 65 "\t" 98 "\t" 27 ... "\n"
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632 [...]
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633
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634 *Note: Make sure the number of columns in the header is identical to the number of columns in the body.*
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635
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636 Design matrix
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637 ^^^^^^^^^^^^^
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638 ::
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639
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640 Sample "\t" Condition "\t" Ethnicity "\t" Patient "\t" Batch "\n"
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641 Sample-1 "\t" Tumor "\t" European "\t" 1 "\t" 1 "\n"
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642 Sample-2 "\t" Normal "\t" European "\t" 1 "\t" 1 "\n"
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643 Sample-3 "\t" Tumor "\t" European "\t" 2 "\t" 1 "\n"
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644 Sample-4 "\t" Normal "\t" European "\t" 2 "\t" 1 "\n"
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645 Sample-5 "\t" Tumor "\t" African "\t" 3 "\t" 1 "\n"
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646 Sample-6 "\t" Normal "\t" African "\t" 3 "\t" 1 "\n"
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647 Sample-7 "\t" Tumor "\t" African "\t" 4 "\t" 2 "\n"
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648 Sample-8 "\t" Normal "\t" African "\t" 4 "\t" 2 "\n"
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649 Sample-9 "\t" Tumor "\t" Asian "\t" 5 "\t" 2 "\n"
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650 Sample-10 "\t" Normal "\t" Asian "\t" 5 "\t" 2 "\n"
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651 Sample-11 "\t" Tumor "\t" Asian "\t" 6 "\t" 2 "\n"
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652 Sample-12 "\t" Normal "\t" Asian "\t" 6 "\t" 2 "\n"
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653
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654 *Note: Avoid factor names that are (1) numerical, (2) contain mathematical symbols and preferebly only use letters.*
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655
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656 Contrast
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657 ^^^^^^^^
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658 The contrast represents the biological question. There can be many questions asked, e.g.:
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659
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660 - Tumor-Normal
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661 - African-European
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662 - 0.5*(Control+Placebo) / Treated
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663
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664 Installation
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665 ------------
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666
116
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667 This tool requires no specific configuration. The following dependencies will installed automatically:
105
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668
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669 - R
108
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670 - limma
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671 - edgeR
105
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672
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673 License
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674 -------
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675 - R
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676 - GPL 2 &amp; GPL 3
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677 - limma
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678 - GPL (&gt;=2)
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679 - edgeR
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680 - GPL (&gt;=2)
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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681
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a02794bb9073 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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682 @CONTACT@
105
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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683 </help>
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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684
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a02794bb9073 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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685 <expand macro="citations" />
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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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686 </tool>