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1 <tool id="idchoice" name="ID choice" version="19.12">
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2 <description>Choosing a particular column in your metadata to be considered as Identifiers</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 IDchoice_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 "$metatype"
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12 col_name "$col_name"
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13 makeunique "$makeunique"
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14
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15 DM_out "$DM_out"
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16 meta_out "$meta_out"
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17
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18 </command>
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19
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20 <inputs>
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21
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22 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
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23 <param name="Metadata_in" type="data" label="Metadata file containing your new IDs" help="Sample metadata or variable metadata" format="tabular" />
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24
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25 <param name="metatype" label="Which ID do you want to change?" type="select" display="radio" help="">
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26 <option value="sample">Samples</option>
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27 <option value="variable" selected="True">Variables</option>
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28 </param>
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29
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30 <param name="col_name" label="Name of the column to consider as new ID" type="text" value="" help="Exact name; must be in your metadata file" />
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31
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32 <param name="makeunique" label="Force unicity if not unique?" type="select" display="radio" help="">
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33 <option value="yes">Yes</option>
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34 <option value="no" selected="True">No</option>
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35 </param>
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36
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37 </inputs>
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38
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39 <outputs>
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40 <data name="DM_out" label="ID_${dataMatrix_in.name}" format="tabular" ></data>
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41 <data name="meta_out" label="ID_${Metadata_in.name}" format="tabular" ></data>
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42 </outputs>
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43
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44
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45 <tests>
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46 <test>
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47 <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
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48 <param name="Metadata_in" value="input_IDc_variableMetadata.txt"/>
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49 <param name="metatype" value="variable"/>
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50 <param name="col_name" value="B"/>
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51 <param name="makeunique" value="yes"/>
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52 <output name="DM_out" file="output1_IDc_dataMatrix.tabular"/>
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53 <output name="meta_out" file="output1_IDc_variableMetadata.tabular"/>
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54 </test>
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55 <test>
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56 <param name="dataMatrix_in" value="input_IDc_dataMatrix.txt"/>
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57 <param name="Metadata_in" value="input_IDc_sampleMetadata.txt"/>
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58 <param name="metatype" value="sample"/>
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59 <param name="col_name" value="AAA"/>
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60 <param name="makeunique" value="yes"/>
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61 <output name="DM_out" file="output2_IDc_dataMatrix.tabular"/>
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62 <output name="meta_out" file="output2_IDc_sampleMetadata.tabular"/>
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63 </test>
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64 </tests>
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65
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66
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67 <help>
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68
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69 .. class:: infomark
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70
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71 **Authors**
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72 | Melanie Petera - PFEM ; INRA ; MetaboHUB
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73
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74 ---------------------------------------------------
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75
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76 ========================
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77 ID Choice
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78 ========================
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79
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80 -----------
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81 Description
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82 -----------
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83
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84 Change the current identifiers into new ones defined in your metadata file.
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85 Can be used for sample ID as well as variable ID.
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86
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87
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88
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89 -----------
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90 Input files
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91 -----------
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92
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93 +----------------------------+---------+
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94 | Parameter : num + label | Format |
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95 +============================+=========+
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96 | 1 : Data matrix file | tabular |
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97 +----------------------------+---------+
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98 | 2 : Metadata file | tabular |
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99 +----------------------------+---------+
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100
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101
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102 Data matrix file contains the intensity values of the variables.
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103 |
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104
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105 Metadata file is meant to be chosen from sample metadata and variable metadata files.
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106 | It should include a column containing your wanted IDs.
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107 |
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108
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109 -----------
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110 Parameters
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111 -----------
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112
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113 Which ID do you want to change?
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114 | This must be consistant with the metadata file you chose as input
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115 |
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116
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117 Name of the column to consider as new ID
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118 | Must be one of your metadata file's column
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119 |
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120
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121 Force unicity if not unique?
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122 | If no (default value), if your ID column does not contain unique values, it will stop the process and send you back an explicit error.
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123 | If yes, non-unique values will be converted by adding "_x" at the end of concerned IDs.
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124 |
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125
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126
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127 -------------
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128 Output files
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129 -------------
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130
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131 ID_metadata
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132 | tabular output
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133 | Corresponds to the input metadata file with new IDs as first column
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134 |
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135
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136 ID_datamatrix
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137 | tabular output
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138 | Corresponds to the input data matrix file with new IDs
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139 |
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140
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141
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142 ---------------------------------------------------
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143
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144 ----------------------
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145 Additional information
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146 ----------------------
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147
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148
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149 .. class:: warningmark
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150
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151 For more information about input files, refer to the corresponding "W4M HowTo" page:
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152 | `W4M table format for Galaxy <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf>`_
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153 |
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154
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155
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156
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157
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158 </help>
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159 </tool> |
