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1 <tool id="generic_filter" name="Generic_Filter" version="2017.04">
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2 <description>Removes elements according to numerical or qualitative values</description>
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3 <command interpreter="Rscript">
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4 filter_wrap.R
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5 dataMatrix_in "$dataMatrix_in"
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6 sampleMetadata_in "$sampleMetadata_in"
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7 variableMetadata_in "$variableMetadata_in"
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8
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9 Numeric "${numeric_condition.Factors}"
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10 #if str($numeric_condition.Factors) == 'TRUE':
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11 #for $i in $numeric_condition.numeric_repeat:
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12 num_file "${i.num_file}"
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13 parm_col "${i.parm_col_num}"
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14 Interval "${i.interval_condition.interval}"
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15 #if str($i.interval_condition.interval) == 'lower':
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16 low_value "${i.interval_condition.low_value}"
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17 #elif str($i.interval_condition.interval) == 'upper':
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18 up_value "${i.interval_condition.up_value}"
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19 #elif str($i.interval_condition.interval) == 'between':
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20 low_value "${i.interval_condition.low_value}"
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21 up_value "${i.interval_condition.up_value}"
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22 #elif str($i.interval_condition.interval) == 'extremity':
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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 #end if
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26 #end for
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27 #end if
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28
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29 Factors "${qualitative_condition.Factors}"
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30 #if str($qualitative_condition.Factors) == 'TRUE':
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31 #for $i in $qualitative_condition.qualitative_repeat:
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32 qual_file "${i.qual_file}"
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33 factor_col "${i.factor_col}"
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34 factors_value "${i.factors_value}"
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35 #end for
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36 #end if
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37
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38 dataMatrix_out "$dataMatrix_out"
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39 sampleMetadata_out "$sampleMetadata_out"
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40 variableMetadata_out "$variableMetadata_out"
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41 </command>
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42
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43 <inputs>
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44 <param name="dataMatrix_in" type="data" label="Data Matrix file" help="" format="tabular" />
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45 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
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46 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
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47
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48 <conditional name="numeric_condition">
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49 <param name="Factors" type="select" label="Deleting samples and/or variables according to Numerical values" help="">
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50 <option value="FALSE">no</option>
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51 <option value="TRUE">yes</option>
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52 </param>
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53 <when value="TRUE">
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54 <repeat name="numeric_repeat" title="Identify the parameter to filter " min="1">
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55 <param name="num_file" label="On file" type="select" display="radio" help="">
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56 <option value="sample">Sample metadata</option>
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57 <option value="variable">Variable metadata</option>
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58 </param>
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59 <param name="parm_col_num" label="Name of the column to filter" type="text" value="" help="" />
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60 <conditional name="interval_condition">
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61 <param name="interval" type="select" label="Interval of values to remove" help="">
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62 <option value="lower">lower</option>
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63 <option value="upper">upper</option>
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64 <option value="between">between</option>
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65 <option value="extremity">extremity</option>
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66 </param>
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67 <when value="lower">
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68 <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/>
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69 </when>
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70 <when value="upper">
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71 <param name="up_value" type="float" label="Remove all values upper than" optional="true" value="0" help=""/>
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72 </when>
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73 <when value="between">
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74 <param name="low_value" type="float" label="Remove all values between" optional="true" value="0" help=""/>
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75 <param name="up_value" type="float" label="And" optional="true" value="1" help=""/>
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76 </when>
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77 <when value="extremity">
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78 <param name="low_value" type="float" label="Remove all values lower than" optional="true" value="0" help=""/>
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79 <param name="up_value" type="float" label="And upper than" optional="true" value="1" help=""/>
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80 </when>
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81 </conditional>
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82 </repeat>
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83 </when>
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84 <when value="FALSE">
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85 </when>
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86 </conditional>
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87
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88 <conditional name="qualitative_condition">
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89 <param name="Factors" type="select" label="Deleting samples and/or variables according to Qualitative values" help="">
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90 <option value="FALSE">no</option>
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91 <option value="TRUE">yes</option>
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92 </param>
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93 <when value="TRUE">
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94 <repeat name="qualitative_repeat" title="Removing a level in factor" min="1">
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95 <param name="qual_file" label="On file" type="select" display="radio" help="">
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96 <option value="sample">Sample metadata</option>
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97 <option value="variable">Variable metadata</option>
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98 </param>
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99 <param name="factor_col" label="Name of the column to filter" type="text" value="" help="" />
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100 <param name="factors_value" type="text" label="Remove factor when" help="" value="" />
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101 </repeat>
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102 </when>
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103 <when value="FALSE">
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104 </when>
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105 </conditional>
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106 </inputs>
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107
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108 <outputs>
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109 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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110 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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111 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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112 </outputs>
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113
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114 <help>
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115
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116 .. class:: infomark
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117
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118 **Authors** Marion Landi and Melanie Petera
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119
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120 ---------------------------------------------------
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121
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122 ==============
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123 Generic_Filter
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124 ==============
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125
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126 -----------
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127 Description
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128 -----------
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129
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130 | Allows to remove all samples and/or variables corresponding to specific values regarding designated factors or numerical variables.
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131 |
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132
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133
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134 -----------------
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135 Workflow position
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136 -----------------
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137
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138
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139 .. image:: filter.png
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140 :width: 800
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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 Input files
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146 -----------
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147
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148 +----------------------------+------------+
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149 | Parameter : num + label | Format |
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150 +============================+============+
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151 | 1 : Data Matrix file | tabular |
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152 +----------------------------+------------+
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153 | 2 : Sample metadata file | tabular |
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154 +----------------------------+------------+
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155 | 3 : Variable metadata file | tabular |
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156 +----------------------------+------------+
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157
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158 |
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159 | 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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160
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161
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162 ----------
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163 Parameters
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164 ----------
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165
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166 Deleting samples and/or variables according to Numerical values:
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167 | If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated
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168 | 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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169 | 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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170 | the corresponding column via the button "Add new Identify the parameter to filter".
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171
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172 | *On file (only if 'yes')*
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173 | Choice between sample and variable filtering (referring to the input file containing the factor).
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174 |
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175
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176 | *Name of the column to filter (only if 'yes')*
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177 | Column name of the numerical parameter from which we want to remove a range of values.
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178 |
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179
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180 | *Interval of values to remove (only if 'yes')*
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181 | Allows to choose which type of interval should be removed:
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182 | - lower: removes all values below a specified value
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183 | - upper: removes all values above a specified value
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184 | - between: removes all values both greater than a specified value and lower than another (upper) one
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185 | - extremity: removes all values that are either lower than a specified value or greater than another (upper) one
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186 |
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187
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188 | *'Remove all values' + interval chosen (only if 'yes')*
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189 | Numerical value(s) used as threshold, depending on the type of interval chosen above.
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190 | Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'.
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191 |
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192
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193 | *Notes:*
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194 | - these parameters can be used several times using the "Add new Identify the parameter to filter" button
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195 | - Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below
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196 |
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197
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198
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199 Deleting samples and/or variables according to Qualitative values
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200 | If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated
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201 | factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field).
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202 | 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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203 | via the button "Add new Removing a level in factor".
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204
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205 | *On file (only if 'yes')*
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206 | Choice between sample and variable filtering (referring to the input file containing the factor).
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207 |
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208
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209 | *Name of the column to filter (only if 'yes')*
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210 | Column name of the factor from which we want to remove a level.
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211 |
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212
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213 | *Remove factor when (only if 'yes')*
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214 | Value that you want to delete from the selected column.
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215 | Each line with that value of designated factor will be deleted.
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216 |
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217
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218 | *Notes:*
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219 | - these parameters can be used several times using the "Add new Removing a level in factor" button
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220 | - this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value
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221 |
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222
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223
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224 ------------
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225 Output files
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226 ------------
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227
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228
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229 dataMatrix
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230 | tabular output
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231 | Identical to the input Data Matrix file with the sample columns and variable lines deleted according to specified filters
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232 |
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233
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234 sampleMetadata
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235 | tabular output
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236 | Identical to the input Sample metadata file with the sample lines deleted according to specified filters
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237 |
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238
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239 variableMetadata
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240 | tabular output
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241 | Identical to the input Variable metadata file with the variable lines deleted according to specified filters
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242 |
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243
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244
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245 ---------------------------------------------------
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246
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247 ---------------
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248 Working example
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249 ---------------
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250
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251
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252 .. class:: warningmark
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253
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254 Soon see the corresponding "Page"
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255
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256 </help>
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257 </tool> |