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1 <tool id="intens_check" name="Intensity Check" version="1.0.1">
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2 <description>Adding informations about intensities in the Variable metadata</description>
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3 <requirements>
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4 <requirement type="package" version="1.1_4">r-batch</requirement>
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5 </requirements>
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6 <command interpreter="Rscript">
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7
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8 wrapper_intensity_check.R
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9
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10 dataMatrix_in "$dataMatrix_in"
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11 sampleMetadata_in "$sampleMetadata_in"
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12 variableMetadata_in "$variableMetadata_in"
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13
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14 class_col "$class_col"
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15
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16 type "${type_cond.type}"
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17 #if $type_cond.type == "One_class" :
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18 class1 "${type_cond.class1}"
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19 #end if
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20
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21 variableMetadata_out "$variableMetadata_out"
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22 graphs_out "$graphs_out"
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23 </command>
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24
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25 <inputs>
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26 <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
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27 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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28 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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29
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30 <param name="class_col" type="data_column" data_ref="sampleMetadata_in" use_header_names="true" label="Class column" help="Class column in Sample metadata" />
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31
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32 <conditional name="type_cond">
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33 <param name="type" type="select" label="Type" display="radio" help="Which class do you want to test ?">
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34 <option value="One_class">Tests between one class and the remaining samples </option>
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35 <option value="Each_class">Tests for each class </option>
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36 </param>
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37 <when value="One_class">
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38 <param name="class1" type="text" label="Selected class" help="This class is the numerator for the fold test" />
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39 </when>
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40 <when value="Each_class">
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41 </when>
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42 </conditional>
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43
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44 </inputs>
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45
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46 <outputs>
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47 <data name="variableMetadata_out" label="IC_${variableMetadata_in.name}" format="tabular" />
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48 <data name="graphs_out" label="IC_Graphs" format="pdf" />
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49 </outputs>
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50
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51 <help>
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52
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53 .. class:: infomark
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54
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55 **Authors**
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56 | Anthony Fernandes - PFEM ; INRA
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57
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58 ---------------------------------------------------
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59
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60 ========================
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61 Intensity Check
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62 ========================
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63
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64 -----------
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65 Description
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66 -----------
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67
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68 This tool performs two tests: the fold calculation, the number and the proportion of missing values.
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69
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70 **Fold:**
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71 The test calculates the ratio between two classes.
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72 In the column name, the first class specified is the one used like numerator for the ratio.
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73
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74 **Missing values:**
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75 This tool calculates the number and the proportion of missing values considering the class.
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76 Missing values in numerical columns of data must be coded NA.
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77
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78 **Two types of tests:**
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79 | - Between **one class** and the remaining samples: if you have only two classes or if you want to test only one class.
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80 | - **Each class**: if the column class contains at least three classes and you want to test each of them.
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81
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82 -----------
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83 Input files
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84 -----------
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85
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86 +----------------------------+------------+
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87 | Parameter | Format |
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88 +============================+============+
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89 | 1 : Data Matrix file | tabular |
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90 +----------------------------+------------+
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91 | 2 : Sample metadata file | tabular |
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92 +----------------------------+------------+
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93 | 3 : Variable metadata file | tabular |
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94 +----------------------------+------------+
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95
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96 ----------
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97 Parameters
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98 ----------
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99
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100 **Class column**
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101 | Select the class column in Sample metadata.
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102
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103 **Type**
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104 | Two options:
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105 | - "One class" allows to perform tests on one class against the remaining samples.
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106 | - "Each class" allows to add several columns with the ratio and the number of missing values for each class.
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107
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108 **Selected class**
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109 | If the type is "one class", specify it to calculate the ratio and the number of missing values.
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110
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111 ------------
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112 Output file
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113 ------------
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114
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115 **Variable metadata file**
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116 | Contains the previous columns in variable metadata and the new ones with fold tests, numbers and proportion of missing values.
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117
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118 **Graphs file**
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119 | Contains barplots with the proportion of NA considering classes and boxplots with the folds values
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120
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121 </help>
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122
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123
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124 </tool>
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125 |
