Mercurial > repos > eschen42 > w4mclstrpeakpics

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planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit ce10bce6cce0a020167f9cf8974fc369eac1228b
author eschen42
date Tue, 20 Jun 2017 03:50:37 -0400
parents 5acad2007e62
children
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1 <tool id="w4mclstrpeakpics" name="View Cluster_Peaks" version="0.98.1">
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2 <description>Visualize sample-cluster peaks</description>
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3
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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 <requirement type="package" version="1.4.2">r-reshape2</requirement>
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8 <requirement type="package" version="0.4_10">r-sqldf</requirement>
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9 <requirement type="package" version="0.98.1">w4mclstrpeakpics</requirement>
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10 </requirements>
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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16
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17 <command detect_errors="exit_code"><![CDATA[
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18 Rscript $__tool_directory__/w4mclstrpeakpics_wrapper.R
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19 data_matrix_path '$dataMatrix_in'
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20 variable_metadata_path '$variableMetadata_in'
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21 sample_metadata_path '$sampleMetadata_in'
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22 sample_selector_column_name '$sampleSelectorColumnName'
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23 sample_selector_value '$sampleSelectorValue'
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24 output_pdf '$outputFigure'
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25 output_tsv '$outputTable'
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26 output_rdata '$outputRdata'
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27 r_package_archive $__tool_directory__/w4mclstrpeakpics_0.98.1.tar.gz
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28 ; echo exit code $?
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29 ]]></command>
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30
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31 <inputs>
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32 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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33 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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34 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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35 <param name="sampleSelectorColumnName" label="Selector-column name" type="text" value = "sampleType" help="Name of column containing selector values." />
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36 <param name="sampleSelectorValue" label="Selector value" type="text" value = "pool" help="Value to match in sample-selector column." />
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37 </inputs>
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38 <outputs>
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39 <data name="outputTable" label="${tool.name}_${sampleSelectorValue}_table" format="tabular" ></data>
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40 <data name="outputFigure" label="${tool.name}_${sampleSelectorValue}_figure" format="pdf" ></data>
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41 <data name="outputRdata" label="${tool.name}_${sampleSelectorValue}_RData" format="rdata" ></data>
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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47 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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48 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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49 <param name="sampleSelectorColumnName" value="sampleType"/>
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50 <param name="sampleSelectorValue" value="pool"/>
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51 <output name="outputTable">
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52 <assert_contents>
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53 <has_text text="0.464572" />
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54 <has_text text="0.114304" />
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55 <has_text text="0.131016" />
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56 <has_text text="0.0701871" />
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57 <has_text text="0.0661764" />
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58 <has_text text="0.0384358" />
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59 <has_text text="0.0614973" />
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60 <has_text text="0.0260695" />
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61 <has_text text="0.0193850" />
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62 <has_text text="0.00835561" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67
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68
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70 <help>
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71 <![CDATA[
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72
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73 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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74
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75 --------------------------------------------------------------------------
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78 **R package**
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80 The *w4mclstrpeakpics* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclstrpeakpics/releases).
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82 -----------------------------------------------------------------------------------------------------------------------------------------
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83
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84
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85 **Tool updates**
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86
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87 See the **NEWS** section at the bottom of this page
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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 Visualize W4M sample-cluster peaks
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93 ==================================
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94
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95 -----------
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96 Description
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97 -----------
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98
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99 Produce a figure to assess the similarities and differences among peaks in a cluster of samples using XCMS-preprocessed data files as input.
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100
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101 -----------------
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102 Workflow Position
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103 -----------------
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104
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105 - Upstream tool category: Preprocessing
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106 - Downstream tool categories: (Not applicable.)
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107
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108 ----------
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109 Motivation
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110 ----------
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111
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112 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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113 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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114 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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115 However, the chromatographic retention time for a chemical can vary from one run to another.
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116 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.
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117
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118 In a typical GC-MS or LC-MS experiment, a pooled sample is repeatedly injected for quality control.
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119 Since this is the same mixture for each injection, the identified peaks would be expected to be identical for all injections.
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120 However, the parameters for peak-picking can exacerbate injection-to-injection variation in performance of the experimental apparatus.
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121 This tool exists to assess the variation in the peaks picked among pooled samples, replicates, or indeed any cluster of samples.
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122
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123 -----------
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124 Input files
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125 -----------
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126
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127 +---------------------------+------------+
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128 | File | Format |
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129 +===========================+============+
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130 | Data matrix | tabular |
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131 +---------------------------+------------+
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132 | Sample metadata | tabular |
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133 +---------------------------+------------+
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134 | Variable metadata | tabular |
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135 +---------------------------+------------+
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136
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137
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138 ----------
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139 Parameters
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140 ----------
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141
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142 Data matrix file
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143 | 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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144 |
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145
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146 Sample metadata file
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147 | 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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148 |
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149
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150 Variable metadata file
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151 | 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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152 |
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153
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154 Selector-column name (default = "sampleType")
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155 | column of W4M/XCMS sampleMetadata holding selector string values.
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156 |
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157
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158 Selector value (default = "pool")
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159 | value within selector column to identify samples for assessment.
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160 |
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161
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162 Include named classes (default = filter-out)
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163 | *filter-in* - include only the named sample classes
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164 | *filter-out* - exclude only the named sample classes
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165 |
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166
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167
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168 Column that names the sample-class (default = 'class')
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169 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
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170 |
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171
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172 Column that names the sample (default = 'sampleMetadata')
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173 | name of the column in sample metadata that has the name of the sample
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174 |
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175
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176
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177 ------------
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178 Output files
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179 ------------
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180
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181
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182 View Cluster_Peaks_<SelectorName>_figure
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183 | (PDF) the output figure, described below.
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184 |
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185
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186 View Cluster_Peaks_<SelectorName>_table
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187 | (tabular separated values) table of the values plotted in the upper-left graph in the output figure.
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188 |
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189
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190 View Cluster_Peaks_<SelectorName>_rdata
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191 | (R data) RData containing all processing and plotting intermediates..
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192 |
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193
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194
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195 ------
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196 Graphs
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197 ------
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198
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199
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200 **The "Feature Number and Likelihood" graph**
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201
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202 The upper left graph in the output figure shows the following:
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203
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204 * The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”).
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205 * For open circles, the Y axis reflects the number of features having the number of samples reflected on the X axis.
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206 * For solid triangles, the Y axis reflects the relative likelihood of features having the number of samples reflected on the X axis, calculated as
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207
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208 .. math:: \frac{(number\hspace{1 mm}of\hspace{1 mm}features) (number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)}{maximum(number\hspace{1 mm}of\hspace{1 mm}samples\hspace{1 mm}per\hspace{1 mm}feature)}
caf0ce49b638 planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
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209
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210 Ideally, there would be an upward trend from left to right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting.
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211
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212
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213 **The "Peak Intensity" graph**
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214
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215 The lower left graph in the output figure presents the data in the upper figure without summarization, so that “the eye” can do the interpretation. It shows the following:
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216
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217 * The X axis reflects the number of samples in which a given feature is present (“the prevalance of a feature among the samples”).
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218 * The Y axis reflects the intensity each sample for each feature having the number of samples reflected on the X axis.
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219
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220 Ideally, there would be an upward trend from left to right, with more points on the right; if not, XCMS peak-picking parameters may need to be adjusted to suppress low-intensity “noise” peaks or to address peak-splitting.
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221
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222
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223 **The "Symbol area/intensity reflect ion intensity" graph**
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224
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225 The upper right graph in the output figure shows the following:
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226
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227 * The X axis reflects the corrected retention time for each feature shown.
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228 * The Y axis reflects the m/z for each feature shown.
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229 * Symbol area reflects intensity for a feature for one sample.
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230 * Overlapping symbols make the overlapping area darker, so the area and darkness reflect the aggregated intensity of a feature. (It is doubtful that a densitometer would be able to recover aggregate intensities accurately from this graph, but philosophically that is how this graph is designed.)
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231 * The graph is not designed to communicate prevalence of a feature among the samples, but the hue of the symbol reflects the prevalance, albeit subtly.
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232
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233 Consequently, if the graph has a lot of large, dark, blueish symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent.
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234
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235
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236 **The "Symbol size/shape reflects prevalence" graph**
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237
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238 By contrast with the area/intensity graph, lower right graph’s primary purpose is to communicate prevalence of a feature among the samples. It`shows the following:
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239
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240 * The X axis reflects the corrected retention time for each feature shown.
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241 * The Y axis reflects the m/z for each feature shown.
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242 * Symbol size and shape reflect the prevalence of a feature among the samples.
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243 * “Vividness” of color reflects the aggregate intensity across all samples for a feature, in an attempt to draw attention to the more intense features.
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244
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245 Consequently, if the graph has a lot of small, vivid symbols for repeated runs of a pooled sample, there is strong evidence that the XCMS peak-picking parameters need adjustment to make peak-picking more consistent.
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246
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247
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248 ---------------
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249 Working example
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250 ---------------
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251
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252 **Input files**
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253
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254 +-------------------+----------------------------------------------------------------------------------------------------------------+
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255 | Input File | Download from URL |
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256 +===================+================================================================================================================+
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257 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_dataMatrix.tsv |
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258 +-------------------+----------------------------------------------------------------------------------------------------------------+
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259 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_sampleMetadata.tsv |
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260 +-------------------+----------------------------------------------------------------------------------------------------------------+
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261 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_variableMetadata.tsv |
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262 +-------------------+----------------------------------------------------------------------------------------------------------------+
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263
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264 **Other input parameters**
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265
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266 +------------------------------------+-----------------+
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267 | Input Parameter | Value |
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268 +====================================+=================+
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269 | Selector-column name | sampleType |
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270 +------------------------------------+-----------------+
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271 | Selector value | pool |
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272 +------------------------------------+-----------------+
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273
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274
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275
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276 ]]>
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277 </help>
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278 <citations>
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279 <citation type="doi">10.1021/ac051437y</citation>
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280 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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281 </citations>
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282 <!--
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283 vim:noet:sw=4:ts=4
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284 --> </tool>