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annotate w4mkmeans.xml @ 0:6ccbe18131a6 draft

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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
author eschen42
date Tue, 08 Aug 2017 15:30:38 -0400
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6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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1 <tool id="w4mkmeans" name="Kmeans_for_W4M" version="0.98.1">
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2 <description>Calculate K-means for dataMatrix features or samples</description>
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4 <requirements>
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5 <requirement type="package" version="3.3.2">r-base</requirement>
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12
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14 <command detect_errors="aggressive"><![CDATA[
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15 Rscript $__tool_directory__/w4mkmeans_wrapper.R
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16 tool_directory $__tool_directory__
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17 data_matrix_path '$dataMatrix_in'
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18 variable_metadata_path '$variableMetadata_in'
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19 sample_metadata_path '$sampleMetadata_in'
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20 ksamples '$ksamples'
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21 kfeatures '$kfeatures'
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22 iter_max '$iter_max'
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23 nstart '$nstart'
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24 algorithm '$algorithm'
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25 scores_out '$scores_out'
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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26 sampleMetadata_out '$sampleMetadata_out'
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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27 variableMetadata_out '$variableMetadata_out'
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28 slots "\${GALAXY_SLOTS:-1}"
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29 ; echo exit code $?
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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30 ]]></command>
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31
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32 <inputs>
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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33 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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34 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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35 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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36 <param name="ksamples" label="K value(s) for samples" type="text" value = "0" help="[ksamples] Single K or comma-separated Ks for samples, or 0 for none." />
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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37 <param name="kfeatures" label="K value(s) for features" type="text" value = "0" help="[kfeatures] Single K or comma-separated Ks for features (variables), or 0 for none." />
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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38 <param name="iter_max" label="Max number of iterations" type="text" value = "10" help="[iter_max] The maximum number of iterations allowed; default 10." />
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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39 <param name="nstart" label="Number of random sets" type="text" value = "1" help="[nstart] How many random sets should be chosen; default 1." />
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40 <param name="algorithm" label="Algorithm for clustering" type="select" value = "Hartigan-Wong" help="[algorithm] K-means clustering algorithm, default 'Hartigan-Wong'; alternatives 'Lloyd', 'MacQueen'; 'Forgy' is a synonym for 'Lloyd', see references for further info.">
6ccbe18131a6 planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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41 <option value="Forgy">Forgy</option>
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42 <option value="Hartigan-Wong" selected="True">Hartigan-Wong</option>
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43 <option value="Lloyd">Lloyd</option>
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44 <option value="MacQueen">MacQueen</option>
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45 </param>
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46 </inputs>
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47
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48 <outputs>
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49 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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50 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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51 <data name="scores_out" label="${tool.name}_${dataMatrix_in.name}.kmeans" format="tabular" ></data>
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52 </outputs>
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53
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54 <tests>
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55 <test>
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56 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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57 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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58 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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59 <param name="ksamples" value="3,4"/>
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60 <param name="kfeatures" value="5,6,7"/>
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61 <param name="iter_max" value="10"/>
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62 <param name="nstart" value="1"/>
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63 <param name="algorithm" value="Hartigan-Wong"/>
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64 <output name="scores_out">
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65 <assert_contents>
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66 <has_text text="proportion" />
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67 <has_text text="0.87482" />
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68 <has_text text="0.89248" />
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69 <has_text text="0.95355" />
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70 <has_text text="0.95673" />
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71 <has_text text="0.95963" />
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72 </assert_contents>
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73 </output>
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74 </test>
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75 </tests>
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76
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77 <help>
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78 <![CDATA[
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79
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80 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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81
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82 ---------------------------------------------------------------------------
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83
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84
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85 **Source** - The source code for the w4mkmeans tool is available (from the Hegeman lab github repository) at https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper
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86
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87 **R code used** - The R code invoked by this wrapper is the R 'stats::kmeans' package
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88
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89 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
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90
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91
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92 **Tool updates**
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93
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94 See the **NEWS** section at the bottom of this page
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95
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96 ---------------------------------------------------
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97
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98 ===========================
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99 K-means for W4M data matrix
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100 ===========================
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101
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102 -----------
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103 Description
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104 -----------
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105
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106 Calculate K-means for sample-clusters (or feature-clusters, or both) using W4M dataMatrix (i.e., XCMS-preprocessed data files) as input.
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107
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108 *Please note that XCMS refers to features as 'variables'. This documentation does not use either term consistently.*
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109
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110
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111 -----------------
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112 Workflow Position
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113 -----------------
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114
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115 - Tool category: Statistical Analysis
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116 - Upstream tool category: Preprocessing
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117 - Downstream tool categories: Statistical Analysis
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118
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119
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120 ----------
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121 Motivation
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122 ----------
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123
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124 This tool clusters samples, features (variables), or both from the W4M dataMatrix and writes the results to new columns in sampleMetadata, variableMetadata, or both, respectively.
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125
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126 - If several, comma-separated K's are supplied, then one column is added for each K.
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127 - This clustering is **not** hierarchical; each member of a cluster is not a member of any other cluster.
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128 - For feature-clustering, each feature is assigned to a cluster such that the feature's response for all samples is closer to the mean of all features for that cluster than to the mean for any other cluster.
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129 - For sample-clustering, each sample is assigned to a cluster such that the sample's response for all features is closer to the mean of all samples for that cluster than to the mean for any other cluster.
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130
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131
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132 -----------
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133 Input files
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134 -----------
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135
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136 +--------------------------------------------+------------+
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137 | File | Format |
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138 +============================================+============+
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139 | Data matrix | tabular |
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140 +--------------------------------------------+------------+
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141 | Sample metadata | tabular |
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142 +--------------------------------------------+------------+
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143 | Variable (i.e., feature) metadata | tabular |
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144 +--------------------------------------------+------------+
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145
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146
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147 ----------
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148 Parameters
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149 ----------
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150
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151 **Data matrix** - input-file dataset
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152
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153 - XCMS 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 feature metadata, respectively (see below)
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154
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155 **Sample metadata** - input-file dataset
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156
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157 - XCMS 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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158
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159 **Feature metadata** - input-file dataset
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160
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161 - XCMS variable x metadata 'variableMetadata' (tabular separated values) file of the numeric and/or character feature metadata, with . as decimal and NA for missing values
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162
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163 **kfeatures** - K or K's for features (default = 0)
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164
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165 - integer or comma-separated integers ; zero (the default) or less will result in no calculation.
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166
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167 **ksamples** - K or K-range for samples (default = 0)
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168
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169 - integer or comma-separated integers ; zero (the default) or less will result in no calculation.
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170
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171 **iter_max** - maximum_iterations (default = 10)
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172
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173 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html).
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174
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175 **nstart** - how many random sets should be chosen (default = 1)
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176
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177 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html).
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178
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179 ------------
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180 Output files
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181 ------------
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182
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183 **XCMS sampleMetadata** - (tabular separated values) file identical to the Sample metadata file given as an input argument, excepting one column added for each K
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184
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185 - **k#** - cluster number for clustering samples with K = #
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186
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187 **XCMS variableMetadata** - (tabular separated values) file identical to the Feature metadata file given as an input argument, excepting one column added for each K
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188
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189 - **k#** - cluster number for clustering features with K = #
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190
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191 **scores** - (tabular separated values) file with one line for each K.
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192
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193 - **clusterOn** - what was clustered - either 'sample' or 'feature'
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194 - **k** - the chosen K for clustering
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195 - **totalSS** - total (*between-treatements* plus total of *within-treatements*) sum of squares
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196 - **betweenSS** - *between-treatements* sum of squares
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197 - **proportion** - betweenSS / totalSS
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198
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199 ---------------
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200 Working example
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201 ---------------
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202
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203 **Input files**
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204
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205 +-------------------+-------------------------------------------------------------------------------------------------------------------+
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206 | Input File | Download from URL |
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207 +===================+===================================================================================================================+
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208 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_dataMatrix.tsv |
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209 +-------------------+-------------------------------------------------------------------------------------------------------------------+
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210 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv |
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211 +-------------------+-------------------------------------------------------------------------------------------------------------------+
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212 | Feature metadata | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_variableMetadata.tsv |
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213 +-------------------+-------------------------------------------------------------------------------------------------------------------+
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214
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215 **Other input parameters**
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216
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217 +-----------------+---------------+
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218 | Input Parameter | Value |
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219 +=================+===============+
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220 | ksamples | 3,4 |
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221 +-----------------+---------------+
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222 | kfeatures | 5,6,7 |
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223 +-----------------+---------------+
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224 | iter_max | 10 |
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225 +-----------------+---------------+
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226 | nstart | 1 |
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227 +-----------------+---------------+
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228 | algorithm | Hartigan-Wong |
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229 +-----------------+---------------+
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230
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231 ----
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232 NEWS
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233 ----
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234
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235 August 2017, Version 0.98.1 - First release
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236
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237 ---------
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238 Citations
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239 ---------
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240
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241 ]]>
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242 </help>
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243 <citations>
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244 <citation type="bibtex"><![CDATA[
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245 @incollection{RCoreTeam2017,
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246 title = {stats::kmeans - K-Means Clustering},
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247 booktitle = {R: A Language and Environment for Statistical Computing},
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248 author = {{R Core Team}},
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249 publisher = {R Foundation for Statistical Computing},
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250 address = {Vienna, Austria},
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251 year = {2017},
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252 url = {https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html},
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253 }
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254 ]]></citation>
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255 <!-- Forgy algorithm -->
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256 <citation type="bibtex"><![CDATA[
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257 @article{forgy65,
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258 added-at = {2006-03-23T12:22:43.000+0100},
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259 author = {Forgy, E.},
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260 biburl = {https://www.bibsonomy.org/bibtex/21e31409932ce91df646c4731350e1207/hotho},
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261 interhash = {c86383cba8cfe00d5e6ef200016aca3f},
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262 intrahash = {1e31409932ce91df646c4731350e1207},
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263 journal = {Biometrics},
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264 keywords = {clustering kmeans},
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265 number = 3,
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266 pages = {768-769},
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267 timestamp = {2006-03-23T12:22:43.000+0100},
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268 title = {Cluster Analysis of Multivariate Data: Efficiency versus Interpretability of Classification},
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269 volume = 21,
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270 year = 1965
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271 }
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272 ]]></citation>
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273 <!-- W4M 3.0 - Guitton et al. 2017-->
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274 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
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275 <!-- W4M 2.5 - Giacomini et al. 2014 -->
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276 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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277 <!-- Hartigan and Wong algorithm -->
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278 <citation type="bibtex"><![CDATA[
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279 @article{Hartigan79,
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diff changeset
280 added-at = {2007-02-27T16:22:09.000+0100},
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281 author = {Hartigan, J. and Wong, M.},
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282 biburl = {https://www.bibsonomy.org/bibtex/23d8bfc440c5725783876929c022f67ce/pierpaolo.pk81},
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283 description = {WSD},
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284 interhash = {10d6d33920d9af578a4d0a556dc1477d},
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diff changeset
285 intrahash = {3d8bfc440c5725783876929c022f67ce},
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286 journal = {Applied Statistics},
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287 keywords = {imported},
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288 pages = {100-108},
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289 timestamp = {2007-02-27T16:22:11.000+0100},
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290 title = {Algorithm AS136: A k-means clustering algorithm},
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291 volume = 28,
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292 year = 1979
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293 }
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294 ]]></citation>
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295 <!-- Lloyd algorithm -->
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296 <citation type="doi">10.1109/TIT.1982.1056489</citation>
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297 <!-- MacQueen algorithm -->
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298 <citation type="bibtex"><![CDATA[
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diff changeset
299 @inproceedings{MacQueen1967,
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300 added-at = {2011-01-11T13:35:01.000+0100},
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301 author = {MacQueen, J. B.},
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302 biburl = {https://www.bibsonomy.org/bibtex/25dcdb8cd9fba78e0e791af619d61d66d/enitsirhc},
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303 booktitle = {Proc. of the fifth Berkeley Symposium on Mathematical Statistics and Probability},
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304 editor = {Cam, L. M. Le and Neyman, J.},
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305 interhash = {8d7d4dfe7d3a06b8c9c3c2bb7aa91e28},
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306 intrahash = {5dcdb8cd9fba78e0e791af619d61d66d},
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307 keywords = {kmeans clustering},
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308 pages = {281-297},
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309 publisher = {University of California Press},
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310 timestamp = {2011-01-11T13:35:01.000+0100},
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311 title = {Some Methods for Classification and Analysis of MultiVariate Observations},
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312 volume = 1,
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313 year = 1967
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314 }
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315 ]]></citation>
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316 </citations>
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317 <!--
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318 vim:et:sw=2:ts=2:
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319 --> </tool>