Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Concatenate_Expression_Matrices.xml @ 124:808ed4b7a4be draft default tip

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author yhoogstrate
date Wed, 08 Feb 2017 10:28:35 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0.b">
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3 <description>Create a full expression matrix by selecting the desired columns from specific count tables</description>
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5 <macros>
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6 <import>edgeR_macros.xml</import>
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7 </macros>
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8
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9 <command>
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10 #set $j = 0
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11 #set $paste = []
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13 #if $add_geneids.choice == "true":
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14 #set $filename = str($j)+".txt"
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15 #set paste = paste + [$filename]
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17 cut -f $add_geneids.column_geneids.value "$add_geneids.sample_geneids" > $filename ;
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18 #set $j += 1
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19 #end if
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21 #for $sample in $samples:
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22 ##echo "$sample.column_index"
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23 ##echo "$sample.column_index.value"
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25 #set $column_str = ",".join([str(x).strip() for x in $sample.column_index.value])
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26 #set $filename = str($j)+".txt"
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27 #set paste = paste + [$filename]
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29 cut -f "$column_str" "$sample.sample" > $filename ;
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30 #set $j += 1
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31 #end for
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33 #if $add_lengths.choice == "true":
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34 #set $filename = str($j)+".txt"
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35 #set paste = paste + [$filename]
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36
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37 cut -f $add_lengths.column_lengths.value "$add_lengths.sample_lengths" > $filename ;
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38 #set $j += 1
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39 #end if
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40
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41 #set $paste_str = " ".join([str(x).strip() for x in $paste])
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42
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43 paste $paste_str > $expression_matrix
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44 </command>
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45
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46 <inputs>
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47 <conditional name="add_geneids">
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48 <param name="choice" type="select" label="Add a gene-IDs column at the end of the file" help="Highly recommended to select!" >
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49 <option value="false">No</option>
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50 <option value="true" selected="true">Yes</option>
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51 </param>
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52 <when value="false" />
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53 <when value="true">
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54 <param name="sample_geneids" type="data" format="tabular"
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55 label="Select Read-count dataset that contains a column for GeneIDs"
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56 help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
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57
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58 <param name="column_geneids"
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59 numerical="false"
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60 use_header_names="true"
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61 label="Select GeneID column"
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62 type="data_column"
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63 data_ref="sample_geneids"
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64 multiple="false">
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65 <validator type="no_options" message="Please select at least one column." />
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66 </param>
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67 </when>
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68 </conditional>
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69
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70 <repeat name="samples" title="Expression Table" help="E.g. a earlier concatenated table, or a HT-seq, featureCounts or DESeq-count result.">
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71 <param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
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72 <!-- select columns -->
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73 <param name="column_index"
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74 numerical="false"
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75 use_header_names="true"
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76 label="Select columns that are associated with this factor level"
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77 type="data_column"
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78 data_ref="sample"
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79 multiple="true">
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80 <validator type="no_options" message="Please select at least one column." />
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81 </param>
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82 </repeat>
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83
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84 <conditional name="add_lengths">
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85 <param name="choice" type="select" label="Add a gene-lengths column at the end of the file" help="Optional, only usefull if RPKM/FPKM calculation is desired." >
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86 <option value="false">No</option>
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87 <option value="true">Yes</option>
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88 </param>
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89 <when value="false" />
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90 <when value="true">
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91 <param name="sample_lengths" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
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92 <param name="column_lengths" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="sample_lengths" multiple="false" size="120">
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93 <validator type="no_options" message="Please select at least one column." />
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94 </param>
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95 </when>
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96 </conditional>
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97
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98 <param name="remove_comment_lines" type="boolean" label="Automatically remove 'comment' lines starting with a '#'" truevale="true" falsevalue="false" selected="true" help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." />
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99
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100 </inputs>
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101
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102 <outputs>
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103 <data format="tabular" name="expression_matrix" label="Expression matrix" />
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104 </outputs>
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105
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106 <tests>
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107 <test>
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108 <conditional name="add_geneids">
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109 <param name="choice" value="true" />
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110 <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
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111 <param name="column_geneids" value="1" />
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112 </conditional>
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113
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114 <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
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115 <param name="samples_0|column_index" value="2" />
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116
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117 <conditional name="add_lengths">
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118 <param name="choice" value="false" />
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119 </conditional>
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120
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121 <param name="remove_comment_lines" value="false" />
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122
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123 <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
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124 </test>
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125 <test>
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126 <conditional name="add_geneids">
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127 <param name="choice" value="true" />
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128 <param name="sample_geneids" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
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129 <param name="column_geneids" value="1" />
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130 </conditional>
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131
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132 <!-- <repeat name="samples"> -->
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133 <param name="samples_0|sample" value="GSE51403/GSE51403_expression_matrix_Control_1.txt" />
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134 <param name="samples_0|column_index" value="2" />
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135 <!-- </repeat> -->
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136
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137 <!-- <repeat name="samples"> -->
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138 <param name="samples_1|sample" value="GSE51403/GSE51403_expression_matrix_Control_2.txt" />
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139 <param name="samples_1|column_index" value="2" />
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140 <!-- </repeat> -->
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141
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142 <!-- <repeat name="samples"> -->
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143 <param name="samples_2|sample" value="GSE51403/GSE51403_expression_matrix_Control_3.txt" />
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144 <param name="samples_2|column_index" value="2" />
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145 <!-- </repeat> -->
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146
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147 <!-- <repeat name="samples"> -->
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148 <param name="samples_3|sample" value="GSE51403/GSE51403_expression_matrix_Control_4.txt" />
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149 <param name="samples_3|column_index" value="2" />
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150 <!-- </repeat> -->
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151
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152 <!-- <repeat name="samples"> -->
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153 <param name="samples_4|sample" value="GSE51403/GSE51403_expression_matrix_Control_5.txt" />
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154 <param name="samples_4|column_index" value="2" />
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155 <!-- </repeat> -->
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156
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157 <!-- <repeat name="samples"> -->
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158 <param name="samples_5|sample" value="GSE51403/GSE51403_expression_matrix_Control_6.txt" />
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159 <param name="samples_5|column_index" value="2" />
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160 <!-- </repeat> -->
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161
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162 <!-- <repeat name="samples"> -->
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163 <param name="samples_6|sample" value="GSE51403/GSE51403_expression_matrix_Control_7.txt" />
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164 <param name="samples_6|column_index" value="2" />
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165 <!-- </repeat> -->
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166
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167 <!-- <repeat name="samples"> -->
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168 <param name="samples_7|sample" value="GSE51403/GSE51403_expression_matrix_E2.txt" />
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169 <param name="samples_7|column_index" value="2,3,4,5,6,7,8" />
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170 <!-- </repeat> -->
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171
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172 <conditional name="add_lengths">
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173 <param name="choice" value="true" />
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174 <param name="sample_lengths" value="GSE51403/GSE51403_expression_matrix_GeneLengths.txt" />
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175 <param name="column_lengths" value="2" />
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176 </conditional>
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178 <param name="remove_comment_lines" value="false" />
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179
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180 <output name="expression_matrix" file="GSE51403/GSE51403_expression_matrix_full.txt" />
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181 </test>
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182 </tests>
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183
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184 <help>
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185 edgeR: Concatenate Expression Matrices
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186 #######################################
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187
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188 Overview
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189 --------
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190
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191 Create subsets from or combined expression matrices.
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192
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193 **Notes**
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194
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195 Make sure the tables have an identical number of columns compared to the number of headers.
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196 If you export tables using R, make sure you set: col.names=NA. Otherwise column may be swapped during concatenation.
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197
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198 Input
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199 -----
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200
108
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201 @CONTACT@
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202 </help>
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203
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204 <expand macro="citations" />
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205 </tool>