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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="design_from_expression_matrix" name="edgeR: Design- from Expression matrix" version="1.0.0.a">
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3 <description>Create design- from an expression matrix</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1.0.0">design_matrix_creator</requirement>
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7 </requirements>
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8
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9 <command interpreter="python">
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10 design_matrix_creator
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11 -c $expression_matrix
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12
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13 #set $unique_columns = []
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14 #for $factor in $treatments:
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15 #for $level in $factor.rep_factorLevel:
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16 #for $val in $level.factorIndex.value:
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17 #if str($val) not in $unique_columns:
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18 #set $unique_columns = $unique_columns + [str($val)]
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19 #end if
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20 #end for
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21 #end for
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22 #end for
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23
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24 #set $unique_columns = " ".join(unique_columns)
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25 -s $unique_columns
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26
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27 -t
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28 #for $factor in $treatments:
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29 #set $factor_str = str($factor.name).encode('base64').replace('\n','')
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30
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31 #for $level in $factor.rep_factorLevel:
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32 #set $factor_str = $factor_str+":"+str($level.factorLevel).encode('base64').replace('\n','')+":"+",".join([str(x).strip() for x in $level.factorIndex.value])
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33 #end for
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34
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35 $factor_str
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36 #end for
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37
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38 #if $choose_blocking.choice == "true"
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39 -b
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40 #for blocking in $choose_blocking.blocking_repeat:
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41 #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','')
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42
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43 #for $block_iter in $blocking.block:
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44 #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value])
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45 #set $blocking_str = $blocking_str+":"+$block_str
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46 #end for
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47
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48 $blocking_str
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49 #end for
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50 #end if
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51
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52 -o $design_matrix
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53 </command>
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54
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55 <inputs>
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56 <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" />
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57
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58 <repeat name="treatments" title="Factor/Condition" min="1">
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59 <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" />
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60 <repeat name="rep_factorLevel" title="Factor level" min="1">
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61 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a condition" help="e.g. Tumor or Normal; Treated, untreaded or placebo. Field must be non-numerical, preferably only letters!!" />
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62 <param name="factorIndex" numerical="false" use_header_names="true" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" multiple="true" size="120" display="checkboxes">
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63 <validator type="no_options" message="Please select at least one column." />
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64 </param>
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65 </repeat>
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66 </repeat>
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67
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68 <conditional name="choose_blocking">
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69 <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" >
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70 <option value="false">No</option>
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71 <option value="true">Yes</option>
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72 </param>
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73 <when value="false" />
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74 <when value="true">
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75 <repeat name="blocking_repeat" title="Blocking condition" min="1">
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76 <param name="blocking_name" type="text" value="" label="Specify a name for a blocking condition" help="e.g.'Patients' or 'Batches'" />
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77 <repeat name="block" title="Block" min="2">
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78 <param name="block_index" label="Select columns that are associated with this factor level" type="data_column" data_ref="expression_matrix" numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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79 <validator type="no_options" message="Please select at least one column." />
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80 </param>
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81 </repeat>
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82 </repeat>
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83 </when>
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84 </conditional>
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85 </inputs>
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86
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87 <outputs>
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88 <data format="tabular" name="design_matrix" label="Design matrix" />
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89 </outputs>
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90
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91
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92 <tests>
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93 <test>
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94 <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
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95
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96 <!-- <repeat name="treatments"> -->
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97 <param name="treatments_0|name" value="Treatment" />
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98 <!-- <repeat name="rep_factorLevel"> -->
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99 <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" />
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100 <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" />
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101 <!-- </repeat> -->
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102 <!-- <repeat name="rep_factorLevel"> -->
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103 <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" />
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104 <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" />
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105 <!-- </repeat> -->
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106 <!-- </repeat> -->
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107
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108 <conditional name="choose_blocking">
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109 <param value="false" />
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110 </conditional>
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111
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112 <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" />
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113 </test>
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114 </tests>
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115
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116 <help>
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117 edgeR: Design- from Expression matrix
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118 #####################################
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119
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120 Overview
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121 --------
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122
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123 Create a design matrix by selecting the desired patients from an
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124 expression matrix.
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125
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126 Input
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127 -----
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128
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129 **References**
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130
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131 The test data is coming from: doi: 10.1093/bioinformatics/btt688.
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132 http://www.ncbi.nlm.nih.gov/pubmed/24319002
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133
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134 Contact
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135 -------
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136
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137 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
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138 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
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139 Research IT (TraIT) project:
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140
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141 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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142
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143 More tools by the Translational Research IT (TraIT) project can be found
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144 in the following toolsheds:
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145
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146 http://toolshed.dtls.nl/
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147
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148 http://toolshed.g2.bx.psu.edu
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149
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150 http://testtoolshed.g2.bx.psu.edu/
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151 </help>
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152
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153 <citations>
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154 <citation type="doi">10.1093/bioinformatics/btp616</citation>
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155 <citation type="doi">10.1093/bioinformatics/btt688</citation>
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156 </citations>
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157 </tool>
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