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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">
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3 <description>Create design- from an expression matrix</description>
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4
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5 <command interpreter="python">
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6 design_matrix_creator.py
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7 -c $expression_matrix
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8
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9 #set $unique_columns = []
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10 #for $factor in $treatments:
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11 #for $level in $factor.rep_factorLevel:
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12 #for $val in $level.factorIndex.value:
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13 #if str($val) not in $unique_columns:
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14 #set $unique_columns = $unique_columns + [str($val)]
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15 #end if
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16 #end for
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17 #end for
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18 #end for
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19
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20 #set $unique_columns = " ".join(unique_columns)
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21 -s $unique_columns
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22
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23 -t
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24 #for $factor in $treatments:
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25 #set $factor_str = str($factor.name).encode('base64').replace('\n','')
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26
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27 #for $level in $factor.rep_factorLevel:
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28 #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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29 #end for
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30
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31 $factor_str
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32 #end for
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33
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34 #if $choose_blocking.choice == "true"
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35 -b
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36 #for blocking in $choose_blocking.blocking_repeat:
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37 #set $blocking_str = str($blocking.blocking_name).encode('base64').replace('\n','')
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38
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39 #for $block_iter in $blocking.block:
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40 #set $block_str = ",".join([str(x).strip() for x in $block_iter.block_index.value])
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41 #set $blocking_str = $blocking_str+":"+$block_str
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42 #end for
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43
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44 $blocking_str
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45 #end for
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46 #end if
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47
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48 -o $contrast_matrix
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49 </command>
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50
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51 <inputs>
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52 <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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53
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54 <repeat name="treatments" title="Factor/Condition" min="1">
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55 <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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56 <repeat name="rep_factorLevel" title="Factor level" min="1">
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57 <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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58 <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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59 <validator type="no_options" message="Please select at least one column." />
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60 </param>
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61 </repeat>
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62 </repeat>
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63
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64 <conditional name="choose_blocking">
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65 <param name="choice" type="select" label="Define blocking (paired or grouped samples)" help="e.g. to remove batch effects" >
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66 <option value="false">No</option>
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67 <option value="true">Yes</option>
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68 </param>
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69 <when value="false" />
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70 <when value="true">
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71 <repeat name="blocking_repeat" title="Blocking condition" min="1">
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72 <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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73 <repeat name="block" title="Block" min="2">
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74 <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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75 <validator type="no_options" message="Please select at least one column." />
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76 </param>
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77 </repeat>
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78 </repeat>
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79 </when>
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80 </conditional>
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81 </inputs>
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82
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83 <outputs>
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84 <data format="tabular" name="design_matrix" label="Design matrix" />
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85 </outputs>
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86
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87 <help>
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88 edgeR: Design- from Expression matrix
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89
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90 **References**
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91
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92 The test data is coming from: doi: 10.1093/bioinformatics/btt688.
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93 http://www.ncbi.nlm.nih.gov/pubmed/24319002
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94 </help>
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95 </tool>
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