Mercurial > repos > yhoogstrate > edger_with_design_matrix
annotate edgeR_Differential_Gene_Expression.xml @ 118:7e98e8bcfbf7 draft
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author | yhoogstrate |
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date | Wed, 09 Dec 2015 10:42:33 -0500 |
parents | 6df940f979c8 |
children | 0a05f6a91d71 |
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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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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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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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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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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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11 </requirements> |
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12 |
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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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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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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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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
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20 level="fatal" |
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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
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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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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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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> /dev/null | grep -v -i "WARNING: ")</version_command> |
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38 |
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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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51 |
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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 |
117
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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 |
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146 output_MDSplot_logFC <- args[9] |
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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") { |
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240 write("Calculating MDS plot (logFC method)",stdout()) |
117
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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 |
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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 |
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281 |
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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 |
117
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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 |
117
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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() |
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311 } |
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312 |
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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 } |
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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 |
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334 bitmap(output_BCVplot,type="png16m",width=10.5*3,height=7*3) |
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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()) |
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343 fit <- glmFit(dge,design) |
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344 |
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345 write(paste("Performing likelihood ratio test: ",contrast,sep=""),stdout()) |
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346 cont <- c(contrast) |
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347 cont <- makeContrasts(contrasts=cont, levels=design) |
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348 |
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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()) |
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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")) |
109
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376 with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red")) |
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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) |
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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/ |
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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 } |
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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)") |
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397 center <- sum(h\$counts) / length(h\$counts) |
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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) |
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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) |
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405 text(0,max(h\$counts),paste("e=",round(rmsd,2),sep=""),pos=4,col="blue") |
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406 ## change e into epsilon somehow |
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407 dev.off() |
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408 } |
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409 } |
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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 { |
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418 ## png(output_heatmap_plot) |
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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 { |
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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 } |
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442 |
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443 mds_distance = as.dist(mds_distance_logFC\$distance.matrix) |
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444 clustering = hclust(mds_distance) |
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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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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 |
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460 <inputs> |
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461 <param name="expression_matrix" type="data" format="tabular" label="Expression (read count) matrix" /> |
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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'." /> |
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463 |
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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." /> |
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465 |
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466 <param name="fdr" type="float" min="0" max="1" value="0.05" label="False Discovery Rate (FDR)" /> |
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467 |
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468 <param name="outputs" type="select" label="Optional desired outputs" multiple="true" display="checkboxes"> |
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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> |
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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> |
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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 |
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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 |
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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 <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
|
490 <data format="tabular" name="output_count_edgeR" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - differentially expressed genes" /> |
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 <data format="tabular" name="output_cpm" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - CPM" /> |
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 |
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 <data format="tabular" name="output_raw_counts" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - raw counts"> |
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 <filter>outputs and ("make_output_raw_counts" 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
|
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
parents:
diff
changeset
|
497 <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
|
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
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
parents:
diff
changeset
|
506 |
117
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
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)"> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
508 <filter>outputs and ("make_output_MDSplot_logFC_coordinates" in outputs)</filter> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
509 </data> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
510 |
105
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 <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
|
512 <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
|
513 |
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
parents:
diff
changeset
|
515 <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
|
516 <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
|
517 <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
|
518 </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
|
519 </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
|
520 |
117
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
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)"> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
522 <filter>outputs and ("make_output_MDSplot_bcv_coordinates" in outputs)</filter> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
523 </data> |
6df940f979c8
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit c7e4f2dfb8c35144b787850b60e116edfbaaa20f
yhoogstrate
parents:
116
diff
changeset
|
524 |
105
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 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
parents:
diff
changeset
|
526 <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
parents:
diff
changeset
|
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
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557 |
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558 <change_format> |
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559 <when input="output_format_images" value="png" format="png" /> |
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560 <when input="output_format_images" value="pdf" format="pdf" /> |
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561 <when input="output_format_images" value="svg" format="svg" /> |
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562 </change_format> |
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563 </data> |
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564 |
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565 <data format="png" name="output_heatmap_plot" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - Heatmap"> |
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566 <filter>outputs and ("make_output_heatmap_plot" in outputs)</filter> |
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567 |
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568 <change_format> |
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569 <when input="output_format_images" value="png" format="png" /> |
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570 <when input="output_format_images" value="pdf" format="pdf" /> |
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571 <when input="output_format_images" value="svg" format="svg" /> |
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572 </change_format> |
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573 </data> |
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574 |
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575 <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object"> |
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576 <filter>outputs and ("make_output_RData_obj" in outputs)</filter> |
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577 </data> |
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578 |
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579 <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" > |
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580 <filter>outputs and ("make_output_R_stdout" in outputs)</filter> |
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581 </data> |
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582 </outputs> |
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583 |
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584 <tests> |
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585 <test> |
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586 <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" /> |
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587 <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.txt" /> |
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588 |
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589 <param name="contrast" value="E-C"/> |
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590 |
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591 <param name="fdr" value="0.05" /> |
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592 |
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593 <param name="output_format_images" value="png" /> |
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594 |
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595 <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.tabular.txt" /> |
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596 </test> |
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597 </tests> |
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598 |
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599 <help> |
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600 edgeR: Differential Gene(Expression) Analysis |
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601 ############################################# |
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602 |
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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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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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628 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
yhoogstrate
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629 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
yhoogstrate
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630 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
yhoogstrate
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631 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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632 [...] |
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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633 |
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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634 *Note: Make sure the number of columns in the header is identical to the number of columns in the body.* |
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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635 |
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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636 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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637 ^^^^^^^^^^^^^ |
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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638 :: |
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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639 |
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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640 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
yhoogstrate
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641 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
yhoogstrate
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642 Sample-2 "\t" Normal "\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
yhoogstrate
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643 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
yhoogstrate
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644 Sample-4 "\t" Normal "\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
yhoogstrate
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645 Sample-5 "\t" Tumor "\t" African "\t" 3 "\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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646 Sample-6 "\t" Normal "\t" African "\t" 3 "\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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647 Sample-7 "\t" Tumor "\t" African "\t" 4 "\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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648 Sample-8 "\t" Normal "\t" African "\t" 4 "\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
yhoogstrate
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649 Sample-9 "\t" Tumor "\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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650 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
yhoogstrate
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651 Sample-11 "\t" Tumor "\t" Asian "\t" 6 "\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
yhoogstrate
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652 Sample-12 "\t" Normal "\t" Asian "\t" 6 "\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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653 |
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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654 *Note: Avoid factor names that are (1) numerical, (2) contain mathematical symbols and preferebly only use letters.* |
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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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655 |
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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656 Contrast |
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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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657 ^^^^^^^^ |
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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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658 The contrast represents the biological question. There can be many questions asked, e.g.: |
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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659 |
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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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660 - Tumor-Normal |
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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661 - African-European |
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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662 - 0.5*(Control+Placebo) / Treated |
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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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663 |
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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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|
664 Installation |
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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665 ------------ |
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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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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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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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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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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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673 License |
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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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674 ------- |
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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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675 - R |
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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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676 - GPL 2 & GPL 3 |
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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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677 - limma |
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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678 - GPL (>=2) |
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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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679 - edgeR |
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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680 - GPL (>=2) |
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681 |
108
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682 @CONTACT@ |
105
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683 </help> |
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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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684 |
108
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685 <expand macro="citations" /> |
105
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686 </tool> |