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1 <tool id="generic_filter" name="Generic_Filter" version="2020.01">
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2 <description>Removes elements according to numerical or qualitative values</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>
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7 Rscript '$__tool_directory__/filter_wrap.R'
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8 dataMatrix_in "$dataMatrix_in"
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9 sampleMetadata_in "$sampleMetadata_in"
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10 variableMetadata_in "$variableMetadata_in"
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11
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12 Numeric "${numeric_condition.Factors}"
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13 #if str($numeric_condition.Factors) == 'TRUE':
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14 #for $i in $numeric_condition.numeric_repeat:
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15 num_file "${i.num_file}"
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16 parm_col "${i.parm_col_num}"
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17 Interval "${i.interval_condition.interval}"
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18 #if str($i.interval_condition.interval) == 'lower':
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19 low_value "${i.interval_condition.low_value}"
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20 #elif str($i.interval_condition.interval) == 'upper':
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21 up_value "${i.interval_condition.up_value}"
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22 #elif str($i.interval_condition.interval) == 'between':
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23 low_value "${i.interval_condition.low_value}"
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24 up_value "${i.interval_condition.up_value}"
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25 #elif str($i.interval_condition.interval) == 'extremity':
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26 low_value "${i.interval_condition.low_value}"
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27 up_value "${i.interval_condition.up_value}"
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28 #end if
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29 #end for
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30 #end if
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31
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32 Factors "${qualitative_condition.Factors}"
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33 #if str($qualitative_condition.Factors) == 'TRUE':
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34 #for $i in $qualitative_condition.qualitative_repeat:
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35 qual_file "${i.qual_file}"
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36 factor_col "${i.factor_col}"
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37 factors_value "${i.factors_value}"
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38 #end for
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39 #end if
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40
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41 dataMatrix_out "$dataMatrix_out"
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42 sampleMetadata_out "$sampleMetadata_out"
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43 variableMetadata_out "$variableMetadata_out"
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44 </command>
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45
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46 <inputs>
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47 <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
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48 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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49 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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50
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51 <conditional name="numeric_condition">
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52 <param name="Factors" type="select" label="Deleting samples and/or variables according to Numerical values" help="">
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53 <option value="FALSE">no</option>
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54 <option value="TRUE">yes</option>
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55 </param>
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56 <when value="TRUE">
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57 <repeat name="numeric_repeat" title="Identify the parameter to filter " min="1">
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58 <param name="num_file" label="On file" type="select" display="radio" help="">
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59 <option value="sample">Sample metadata</option>
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60 <option value="variable">Variable metadata</option>
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61 </param>
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62 <param name="parm_col_num" label="Name of the column to filter" type="text" value="" help="" />
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63 <conditional name="interval_condition">
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64 <param name="interval" type="select" label="Interval of values to remove" help="">
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65 <option value="lower">lower</option>
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66 <option value="upper">upper</option>
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67 <option value="between">between</option>
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68 <option value="extremity">extremity</option>
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69 </param>
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70 <when value="lower">
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71 <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/>
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72 </when>
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73 <when value="upper">
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74 <param name="up_value" type="float" label="Remove all values upper than" optional="true" value="0" help=""/>
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75 </when>
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76 <when value="between">
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77 <param name="low_value" type="float" label="Remove all values between" optional="true" value="0" help=""/>
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78 <param name="up_value" type="float" label="And" optional="true" value="1" help=""/>
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79 </when>
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80 <when value="extremity">
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81 <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/>
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82 <param name="up_value" type="float" label="And upper than" optional="true" value="1" help=""/>
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83 </when>
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84 </conditional>
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85 </repeat>
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86 </when>
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87 <when value="FALSE">
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88 </when>
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89 </conditional>
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90
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91 <conditional name="qualitative_condition">
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92 <param name="Factors" type="select" label="Deleting samples and/or variables according to Qualitative values" help="">
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93 <option value="FALSE">no</option>
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94 <option value="TRUE">yes</option>
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95 </param>
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96 <when value="TRUE">
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97 <repeat name="qualitative_repeat" title="Removing a level in factor" min="1">
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98 <param name="qual_file" label="On file" type="select" display="radio" help="">
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99 <option value="sample">Sample metadata</option>
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100 <option value="variable">Variable metadata</option>
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101 </param>
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102 <param name="factor_col" label="Name of the column to filter" type="text" value="" help="" />
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103 <param name="factors_value" type="text" label="Remove factor when" help="" value="" />
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104 </repeat>
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105 </when>
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106 <when value="FALSE">
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107 </when>
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108 </conditional>
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109 </inputs>
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110
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111 <outputs>
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112 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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113 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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114 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 <param name="dataMatrix_in" value="in_DM1.tabular"/>
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120 <param name="sampleMetadata_in" value="in_SM1.tabular"/>
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121 <param name="variableMetadata_in" value="in_VM1.tabular"/>
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122 <conditional name="numeric_condition">
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123 <param name="Factors" value="TRUE"/>
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124 <param name="numeric_repeat_0|num_file" value="variable"/>
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125 <param name="numeric_repeat_0|parm_col_num" value="rt"/>
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126 <param name="numeric_repeat_0|interval_condition|interval" value="lower"/>
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127 <param name="numeric_repeat_0|interval_condition|low_value" value="1.2"/>
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128 </conditional>
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129 <conditional name="qualitative_condition">
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130 <param name="Factors" value="TRUE"/>
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131 <param name="qualitative_repeat_0|qual_file" value="sample"/>
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132 <param name="qualitative_repeat_0|factor_col" value="Time"/>
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133 <param name="qualitative_repeat_0|factors_value" value="3"/>
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134 </conditional>
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135 <output name="dataMatrix_out" file="out_DM1.tabular"/>
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136 <output name="sampleMetadata_out" file="out_SM1.tabular"/>
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137 <output name="variableMetadata_out" file="out_VM1.tabular"/>
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138 </test>
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139 </tests>
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140
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141 <help>
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142
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143 .. class:: infomark
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144
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145 **Authors:**
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146 Melanie Petera for original R code - Marion Landi and Melanie Petera for original Galaxy wrapper
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147 **Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
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148
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149 ---------------------------------------------------
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150
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151 ==============
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152 Generic Filter
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153 ==============
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154
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155 -----------
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156 Description
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157 -----------
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158
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159 | Allows to remove all samples and/or variables corresponding to specific values regarding designated factors or numerical variables.
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160 |
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161
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162
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163 -----------------
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164 Workflow position
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165 -----------------
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166
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167
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168 .. image:: filter.png
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169 :width: 700
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170
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171
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172
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173 -----------
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174 Input files
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175 -----------
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176
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177 +----------------------------+------------+
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178 | Parameter : num + label | Format |
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179 +============================+============+
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180 | 1 : Data matrix file | tabular |
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181 +----------------------------+------------+
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182 | 2 : Sample metadata file | tabular |
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183 +----------------------------+------------+
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184 | 3 : Variable metadata file | tabular |
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185 +----------------------------+------------+
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186
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187 |
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188 | Missing values in numerical columns of data must be coded NA if you want to use the Numerical filter on them.
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189
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190
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191 ----------
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192 Parameters
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193 ----------
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194
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195 Deleting samples and/or variables according to Numerical values:
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196 | If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated
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197 | numerical parameter ("Name of the column to remove" field) equals the selected range of values (depending on the "Interval of values to remove" chosen).
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198 | To delete multiple independent intervals of value from the same parameter, it is necessary to add as many times as necessary
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199 | the corresponding column via the "Insert Identify the parameter to filter" button.
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200
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201 | *On file (only if 'yes')*
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202 | Choice between sample and variable filtering (referring to the input file containing the factor).
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203 |
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204
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205 | *Name of the column to filter (only if 'yes')*
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206 | Column name of the numerical parameter from which we want to remove a range of values.
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207 |
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208
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209 | *Interval of values to remove (only if 'yes')*
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210 | Allows to choose which type of interval should be removed:
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211 | - lower: removes all values below a specified value
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212 | - upper: removes all values above a specified value
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213 | - between: removes all values both greater than a specified value and lower than another (upper) one
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214 | - extremity: removes all values that are either lower than a specified value or greater than another (upper) one
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215 |
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216
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217 | *'Remove all values' + interval chosen (only if 'yes')*
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218 | Numerical value(s) used as threshold, depending on the type of interval chosen above.
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219 | Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'.
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220 |
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221
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222 | *Notes:*
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223 | - these parameters can be used several times using the "Insert Identify the parameter to filter" button
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224 | - Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below
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225 |
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226
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227
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228 Deleting samples and/or variables according to Qualitative values
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229 | If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated
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230 | factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field).
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231 | To delete multiple values of the same factor, it is necessary to add as many times as necessary the corresponding factor
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232 | via the "Insert Removing a level in factor" button.
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233
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234 | *On file (only if 'yes')*
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235 | Choice between sample and variable filtering (referring to the input file containing the factor).
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236 |
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237
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238 | *Name of the column to filter (only if 'yes')*
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239 | Column name of the factor from which we want to remove a level.
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240 |
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241
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242 | *Remove factor when (only if 'yes')*
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243 | Value that you want to delete from the selected column.
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244 | Each line with that value of designated factor will be deleted.
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245 |
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246
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247 | *Notes:*
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248 | - these parameters can be used several times using the "Insert Removing a level in factor" button
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249 | - this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value
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250 |
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251
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252
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253 ------------
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254 Output files
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255 ------------
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256
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257
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258 dataMatrix
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259 | tabular output
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260 | Identical to the input Data matrix file with the sample columns and variable lines deleted according to specified filters
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261 |
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262
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263 sampleMetadata
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264 | tabular output
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265 | Identical to the input Sample metadata file with the sample lines deleted according to specified filters
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266 |
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267
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268 variableMetadata
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269 | tabular output
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270 | Identical to the input Variable metadata file with the variable lines deleted according to specified filters
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271 |
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272
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273
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274 ---------------------------------------------------
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275
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276 ----------------------
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277 Additional information
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278 ----------------------
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279
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280
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281 .. class:: warningmark
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282
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283 For more information about input files, refer to the corresponding "W4M HowTo" page:
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284 | `W4M table format for Galaxy <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf>`_
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285 |
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286
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287
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288
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289 </help>
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290 <citations>
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291 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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292 </citations>
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293 </tool> |
