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1 <tool id="tablemerge" name="Table Merge" version="1.0.1">
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2 <description>Merging dataMatrix with a metadata table</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 tablemerge_wrap.R
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8 dataMatrix_in "$dataMatrix_in"
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9 Metadata_in "$Metadata_in"
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10
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11 metatype "$metatype"
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12
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13 combined_out "$combined_out"
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14
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15 </command>
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16
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17 <inputs>
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18 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
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19 <param name="Metadata_in" type="data" label="Metadata file" help="Sample metadata or variable metadata" format="tabular" />
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20
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21 <param name="metatype" label="Type of metadata" type="select" display="radio" help="">
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22 <option value="sample">Sample metadata</option>
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23 <option value="variable">Variable metadata</option>
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24 </param>
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25
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26 </inputs>
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27
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28 <outputs>
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29 <data name="combined_out" label="Combined_${Metadata_in.name}" format="tabular" ></data>
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30 </outputs>
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31
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32 <tests>
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33 <test>
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34 <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
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35 <param name="Metadata_in" value="input_TM1_variableMetadata.txt"/>
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36 <param name="metatype" value="variable"/>
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37 <output name="combined_out" file="output_TM1_expected.tabular"/>
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38 </test>
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39 <test>
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40 <param name="dataMatrix_in" value="input_TM12_dataMatrix.txt"/>
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41 <param name="Metadata_in" value="input_TM2_sampleMetadata.txt"/>
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42 <param name="metatype" value="sample"/>
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43 <output name="combined_out" file="output_TM2_expected.tabular"/>
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44 </test>
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45 </tests>
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46
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47
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48 <help>
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49
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50 .. class:: infomark
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51
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52 **Authors**
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53 | Melanie Petera - PFEM ; INRA ; MetaboHUB
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54
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55 ---------------------------------------------------
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56
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57 ========================
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58 Table Merge
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59 ========================
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60
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61 -----------
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62 Description
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63 -----------
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64
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65 Merges the data matrix with a selected metadata file (sample metadata or variable metadata)
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66 to obtain a single file.
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67
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68
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69
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70 -----------
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71 Input files
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72 -----------
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73
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74 +----------------------------+---------+
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75 | Parameter : num + label | Format |
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76 +============================+=========+
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77 | 1 : Data matrix file | tabular |
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78 +----------------------------+---------+
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79 | 2 : Metadata file | tabular |
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80 +----------------------------+---------+
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81
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82
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83 Data matrix file contains the intensity values of the variables.
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84 |
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85
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86 Metadata file is meant to be chosen from sample metadata and variable metadata files.
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87 |
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88
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89 ----------
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90 Parameter
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91 ----------
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92
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93 Type of metadata
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94 | Specify which type of metadata table is given as Metadata file
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95 |
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96
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97
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98 ------------
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99 Output file
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100 ------------
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101
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102
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103 Combined_Metadata
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104 | tabular output
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105 | Corresponds to the input metadata file completed as new columns by the intensities in the input data matrix file
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106 |
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107
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108
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109 ---------------------------------------------------
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110
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111
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112 .. class:: warningmark
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113
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114 For more information about input files, refer to the corresponding "W4M HowTo" page:
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115 | `W4M table format for Galaxy <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf>`_
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116 |
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117
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118
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119
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120
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121 </help>
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122 </tool> |
