Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 3:191a720488ce draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
author eschen42
date Thu, 11 May 2017 00:05:51 -0400
parents 23c6d271def9
children 499c7ecfa834
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191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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1 <tool id="w4mclassfilter" name="Sample_Subset" version="0.98.1">
0
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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 ]]></command>
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28
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29 <inputs>
2
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30 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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31 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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32 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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33 <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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34 <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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35 <option value="TRUE">filter-in</option>
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36 <option value="FALSE" selected="true">filter-out</option>
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37 </param>
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38 <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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39 <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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40 </inputs>
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41 <outputs>
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42 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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43 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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44 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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45 </outputs>
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46
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47 <tests>
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48 <test>
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49 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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50 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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51 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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52 <param name="classnameColumn" value="gender"/>
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53 <param name="sampleclassNames" value="M"/>
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54 <param name="samplenameColumn" value="sampleMetadata"/>
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55 <param name="inclusive" value="filter-in"/>
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56 <output name="dataMatrix_out">
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57 <assert_contents>
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58 <not_has_text text="HU_028" />
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69 <has_text text="HU_017" />
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70 <has_text text="HU_034" />
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71 <has_text text="HU_078" />
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72 <has_text text="HU_091" />
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73 <has_text text="HU_093" />
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74 <has_text text="HU_099" />
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75 <has_text text="HU_130" />
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76 <has_text text="HU_134" />
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77 <has_text text="HU_138" />
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78 <has_text text="HMDB03193" />
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79 <not_has_text text="HMDB00822" />
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80 <has_text text="HMDB01101" />
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81 <has_text text="HMDB01101.1" />
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82 <has_text text="HMDB10348" />
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83 <has_text text="HMDB59717" />
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84 <has_text text="HMDB13189" />
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85 <has_text text="HMDB00299" />
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86 <has_text text="HMDB00191" />
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87 <has_text text="HMDB00518" />
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88 <has_text text="HMDB00715" />
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89 <has_text text="HMDB01032" />
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90 <has_text text="HMDB00208" />
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91 <has_text text="HMDB04824" />
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92 <has_text text="HMDB00512" />
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93 <has_text text="HMDB00251" />
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94 </assert_contents>
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95 </output>
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96 </test>
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97 <test>
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98 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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99 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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100 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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101 <param name="classnameColumn" value="gender"/>
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102 <param name="sampleclassNames" value="M"/>
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103 <param name="samplenameColumn" value="sampleMetadata"/>
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104 <param name="inclusive" value="filter-in"/>
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105 <output name="sampleMetadata_out">
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106 <assert_contents>
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107 <not_has_text text="HU_028" />
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108 <not_has_text text="HU_051" />
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109 <not_has_text text="HU_060" />
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125 <has_text text="HU_134" />
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126 <has_text text="HU_138" />
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127 </assert_contents>
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128 </output>
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129 </test>
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130 <test>
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131 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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132 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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133 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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134 <param name="classnameColumn" value="gender"/>
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135 <param name="sampleclassNames" value="M"/>
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136 <param name="samplenameColumn" value="sampleMetadata"/>
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137 <param name="inclusive" value="filter-in"/>
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138 <output name="variableMetadata_out">
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139 <assert_contents>
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140 <has_text text="HMDB03193" />
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141 <not_has_text text="HMDB00822" />
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142 <has_text text="HMDB01101" />
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143 <has_text text="HMDB01101.1" />
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144 <has_text text="HMDB10348" />
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146 <has_text text="HMDB13189" />
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151 <has_text text="HMDB01032" />
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152 <has_text text="HMDB00208" />
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153 <has_text text="HMDB04824" />
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154 <has_text text="HMDB00512" />
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155 <has_text text="HMDB00251" />
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156 </assert_contents>
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157 </output>
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158 </test>
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159 </tests>
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160
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161
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162
2
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163 <help>
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164 <![CDATA[
0
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165
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166 .. class:: infomark
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167
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168 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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169
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170 --------------------------------------------------------------------------
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171
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172 .. class:: infomark
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173
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174 **R package**
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175
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176 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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177
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178 -----------------------------------------------------------------------------------------------------------------------------------------
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179
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180 .. class:: infomark
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181
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182 **Tool updates**
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183
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184 See the **NEWS** section at the bottom of this page
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185
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186 ---------------------------------------------------
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187
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188 ==============================================
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189 Filter Workflow4Metabolomics data matrix files
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190 ==============================================
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191
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192 -----------
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193 Description
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194 -----------
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195
3
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196 Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class
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197
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198 -----------------
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199 Workflow Position
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200 -----------------
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201
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202 - Upstream tool category: Preprocessing
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203 - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control
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204
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205 ----------
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206 Motivation
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207 ----------
0
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208
3
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209 GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio.
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210 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time.
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211 Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ.
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212 However, the chromatographic retention time for a chemical can vary from one run to another.
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213 In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included.
0
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214
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215 Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant.
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216 Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters.
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217 Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance.
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218
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219 The w4mclassfilter tool provides a way to choose subsets of samples for further analysis.
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220 The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples.
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221 The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis.
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222 Class-values to be considered are provided by the user as a comma-separated list.
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223 The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out").
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224 Next, missing and negative intensites for features of the remaining samples are imputed to zero.
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225 Finally, samples or features with zero variance are eliminated.
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226
0
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227
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228 -----------
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229 Input files
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230 -----------
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231
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232 +---------------------------+------------+
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233 | File | Format |
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234 +===========================+============+
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235 | Data matrix | tabular |
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236 +---------------------------+------------+
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237 | Sample metadata | tabular |
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238 +---------------------------+------------+
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239 | Variable metadata | tabular |
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240 +---------------------------+------------+
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241
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242
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243 ----------
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244 Parameters
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245 ----------
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246
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247 Data matrix file
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248 | variable x sample **dataMatrix** (tabular separated values) 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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249 |
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250
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251 Sample metadata file
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252 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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253 |
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254
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255 Variable metadata file
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256 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
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257 |
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258
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259 Names of sample classes (default = no names)
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260 | comma-separated names of sample classes to include or exclude
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261 |
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262
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263 Include named classes (default = filter-out)
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264 | *filter-in* - include only the named sample classes
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265 | *filter-out* - exclude only the named sample classes
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266 |
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267
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268
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269 Column that names the sample-class (default = 'class')
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270 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
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271 |
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272
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273 Column that names the sample (default = 'sampleMetadata')
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274 | name of the column in sample metadata that has the name of the sample
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275 |
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276
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277
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278 ------------
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279 Output files
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280 ------------
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281
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282
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283 sampleMetadata
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284 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
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285 |
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286
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287 variableMetadata
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288 | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
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289 |
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290
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291 dataMatrix
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292 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
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293 |
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294
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295
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296 ---------------
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297 Working example
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298 ---------------
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299
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300 .. class:: infomark
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301
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302 **Input files**
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303
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304 +-------------------+--------------------------------------------------------------------------------------------------------------+
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305 | Input File | Download from URL |
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306 +===================+==============================================================================================================+
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307 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv |
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308 +-------------------+--------------------------------------------------------------------------------------------------------------+
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309 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv |
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310 +-------------------+--------------------------------------------------------------------------------------------------------------+
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311 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv |
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312 +-------------------+--------------------------------------------------------------------------------------------------------------+
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313
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314 .. class:: infomark
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315
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316 **Other input parameters**
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317
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318 +------------------------------------+-----------------+
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319 | Input Parameter | Value |
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320 +====================================+=================+
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321 | Names of sample classes | M |
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322 +------------------------------------+-----------------+
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323 | Include named classes | filter-in |
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324 +------------------------------------+-----------------+
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325 | Column that names the sample-class | gender |
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326 +------------------------------------+-----------------+
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327 | Column that names the sample | sampleMetadata |
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328 +------------------------------------+-----------------+
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329
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330 .. class:: infomark
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331
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332 **Expected outputs**
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333
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334 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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335 | Expected Output | Download from URL |
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336 +===================+=================================================================================================================+
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337 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv |
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338 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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339 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv |
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340 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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341 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv |
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342 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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343
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344
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345 -----------------------------------------------------------------------------
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346
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347 ----
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348 NEWS
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349 ----
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350
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351 CHANGES IN VERSION 0.98.1
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352 =========================
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353
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354 NEW FEATURES
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355
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356 First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
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357
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358 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
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359 *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file
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360 *variableMetadata* *is* modified by the tool, so it *does* appear as an output file
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361
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362 INTERNAL MODIFICATIONS
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363
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364 none
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365
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366 ]]>
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367 </help>
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368 <citations>
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369 <citation type="doi">10.1021/ac051437y</citation>
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370 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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371 </citations>
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372 <!--
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373 vim:noet:sw=4:ts=4
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374 --> </tool>