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1 <tool id="W4MClassFilter" name="W4MClassFilter" version="0.98.1">
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2 <description>Filter W4M data by sample class</description>
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3
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4 <requirements>
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5 <requirement type="package" version="3.3.1">r-base</requirement>
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
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7 <requirement type="package" version="0.98.1">w4mclassfilter</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13
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14
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15 <command detect_errors="aggressive"><![CDATA[
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16 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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17 dataMatrix_in "$dataMatrix_in"
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18 sampleMetadata_in "$sampleMetadata_in"
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19 variableMetadata_in "$variableMetadata_in"
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20 sampleclassNames "$sampleclassNames"
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21 inclusive "$inclusive"
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22 classnameColumn "$classnameColumn"
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23 samplenameColumn "$samplenameColumn"
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24 dataMatrix_out "$dataMatrix_out"
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25 sampleMetadata_out "$sampleMetadata_out"
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26 variableMetadata_out "$variableMetadata_out"
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27 information "$information"
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28 ]]></command>
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29
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30 <inputs>
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31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
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32 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
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33 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
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34 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names of sample classes to filter in or out; defaults to no names" />
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35 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
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36 <option value="TRUE">filter-in</option>
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37 <option value="FALSE" selected="true">filter-out</option>
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38 </param>
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39 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
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40 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in sample metadata that has the name of the sample - defaults to 'sampleMetadata'" />
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41 </inputs>
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42 <outputs>
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43 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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44 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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45 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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46 <data name="information" label="${tool.name}__information.txt" format="txt"/>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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52 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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53 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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54 <param name="classnameColumn" value="gender"/>
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55 <param name="sampleclassNames" value="M"/>
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56 <param name="samplenameColumn" value="sampleMetadata"/>
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57 <param name="inclusive" value="filter-in"/>
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58 <param name="information" value="test-information.txt"/>
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59 <output name="dataMatrix_out">
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60 <assert_contents>
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61 <not_has_text text="HU_028" />
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62 <not_has_text text="HU_051" />
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63 <not_has_text text="HU_060" />
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64 <not_has_text text="HU_110" />
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65 <not_has_text text="HU_149" />
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66 <not_has_text text="HU_152" />
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67 <not_has_text text="HU_175" />
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68 <not_has_text text="HU_178" />
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69 <not_has_text text="HU_185" />
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70 <not_has_text text="HU_204" />
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71 <not_has_text text="HU_208" />
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72 <has_text text="HU_017" />
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73 <has_text text="HU_034" />
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74 <has_text text="HU_078" />
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75 <has_text text="HU_091" />
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76 <has_text text="HU_093" />
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77 <has_text text="HU_099" />
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78 <has_text text="HU_130" />
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79 <has_text text="HU_134" />
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80 <has_text text="HU_138" />
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81 <has_text text="HMDB03193" />
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82 <not_has_text text="HMDB00822" />
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83 <has_text text="HMDB01101" />
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84 <has_text text="HMDB01101.1" />
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85 <has_text text="HMDB10348" />
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86 <has_text text="HMDB59717" />
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87 <has_text text="HMDB13189" />
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88 <has_text text="HMDB00299" />
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89 <has_text text="HMDB00191" />
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90 <has_text text="HMDB00518" />
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91 <has_text text="HMDB00715" />
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92 <has_text text="HMDB01032" />
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93 <has_text text="HMDB00208" />
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94 <has_text text="HMDB04824" />
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95 <has_text text="HMDB00512" />
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96 <has_text text="HMDB00251" />
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97 </assert_contents>
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98 </output>
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99 </test>
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100 <test>
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101 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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102 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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103 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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104 <param name="classnameColumn" value="gender"/>
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105 <param name="sampleclassNames" value="M"/>
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106 <param name="samplenameColumn" value="sampleMetadata"/>
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107 <param name="inclusive" value="filter-in"/>
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108 <param name="information" value="test-information.txt"/>
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109 <output name="sampleMetadata_out">
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110 <assert_contents>
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111 <not_has_text text="HU_028" />
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112 <not_has_text text="HU_051" />
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113 <not_has_text text="HU_060" />
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114 <not_has_text text="HU_110" />
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115 <not_has_text text="HU_149" />
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116 <not_has_text text="HU_152" />
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117 <not_has_text text="HU_175" />
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118 <not_has_text text="HU_178" />
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119 <not_has_text text="HU_185" />
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120 <not_has_text text="HU_204" />
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121 <not_has_text text="HU_208" />
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122 <has_text text="HU_017" />
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123 <has_text text="HU_034" />
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124 <has_text text="HU_078" />
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125 <has_text text="HU_091" />
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126 <has_text text="HU_093" />
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127 <has_text text="HU_099" />
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128 <has_text text="HU_130" />
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129 <has_text text="HU_134" />
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130 <has_text text="HU_138" />
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131 </assert_contents>
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132 </output>
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133 </test>
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134 <test>
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135 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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136 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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137 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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138 <param name="classnameColumn" value="gender"/>
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139 <param name="sampleclassNames" value="M"/>
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140 <param name="samplenameColumn" value="sampleMetadata"/>
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141 <param name="inclusive" value="filter-in"/>
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142 <param name="information" value="test-information.txt"/>
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143 <output name="variableMetadata_out">
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144 <assert_contents>
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145 <has_text text="HMDB03193" />
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146 <not_has_text text="HMDB00822" />
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147 <has_text text="HMDB01101" />
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148 <has_text text="HMDB01101.1" />
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149 <has_text text="HMDB10348" />
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150 <has_text text="HMDB59717" />
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151 <has_text text="HMDB13189" />
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152 <has_text text="HMDB00299" />
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153 <has_text text="HMDB00191" />
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154 <has_text text="HMDB00518" />
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155 <has_text text="HMDB00715" />
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156 <has_text text="HMDB01032" />
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157 <has_text text="HMDB00208" />
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158 <has_text text="HMDB04824" />
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159 <has_text text="HMDB00512" />
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160 <has_text text="HMDB00251" />
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161 </assert_contents>
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162 </output>
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163 </test>
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164 </tests>
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165
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166
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167
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168 <help>
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169
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170 .. class:: infomark
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171
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172 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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173
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174 --------------------------------------------------------------------------
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175
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176 .. class:: infomark
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177
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178 **R package**
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179
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180 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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181
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182 -----------------------------------------------------------------------------------------------------------------------------------------
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183
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184 .. class:: infomark
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185
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186 **Tool updates**
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187
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188 See the **NEWS** section at the bottom of this page
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189
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190 ---------------------------------------------------
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191
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192 ==============================================
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193 Filter Workflow4Metabolomics data matrix files
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194 ==============================================
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195
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196 -----------
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197 Description
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198 -----------
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199
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200 Filter set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample class
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201
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202 --------
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203 Comments
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204 --------
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205
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206 The *inclusive* parameter indicates:
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207 - when 'filter-in', that only the sample-classes named should be included
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208 - when 'filter-out', that all sample-classes should be included excepting the sample-classes named
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209
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210 -----------
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211 Input files
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212 -----------
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213
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214 +---------------------------+------------+
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215 | File | Format |
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216 +===========================+============+
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217 | 1) Data matrix | tabular |
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218 +---------------------------+------------+
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219 | 2) Sample metadata | tabular |
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220 +---------------------------+------------+
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221 | 3) Variable metadata | tabular |
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222 +---------------------------+------------+
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223
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224
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225 ----------
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226 Parameters
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227 ----------
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228
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229 Data matrix file
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230 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
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231 |
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232
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233 Sample metadata file
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234 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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235 |
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236
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237 Variable metadata file
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238 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
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239 |
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240
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241 Names of sample classes (default = no names)
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242 | comma-separated names of sample classes to include or exclude
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243 |
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244
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245 Include named classes (default = filter-out)
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246 | *filter-in* - include only the named sample classes
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247 | *filter-out* - exclude only the named sample classes
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248 |
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249
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250 Column that names the sample-class (default = 'class')
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251 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
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252 |
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253
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254 Column that names the sample (default = 'sampleMetadata')
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255 | name of the column in sample metadata that has the name of the sample
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256 |
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257
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258
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259 ------------
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260 Output files
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261 ------------
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262
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263
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264 sampleMetadata_out.tabular
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265 | **sampleMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for samples that have been filtered out
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266 |
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267
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268 variableMetadata_out.tabular
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269 | **variableMetadata** tabular separated file identical to the file given as argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
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270 |
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271
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272 dataMatrix_out.tabular
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273 | **dataMatrix** tabular separated file identical to the file given as argument, excepting lacking columns for samples that have been filtered out (because of the sample-classes specified in the input parameters) and rows for variables (xC-MS features) that have been filtered out (because of zero variance)
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274 |
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275
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276 information.txt
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277 | Text file with all messages and warnings generated during the computation
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278 |
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279
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280 -----------------------------------------------------------------------------
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281
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282 ----
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283 NEWS
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284 ----
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285
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286 CHANGES IN VERSION 0.98.1
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287 =========================
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288
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289 NEW FEATURES
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290
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291 First release - R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
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292
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293 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
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294
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295 INTERNAL MODIFICATIONS
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296
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297 none
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298
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299 </help>
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300 <citations>
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301 </citations>
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302 </tool>
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303 <!-- vim: et sw=2 ts=2 :
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304 -->
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