Mercurial > repos > eschen42 > w4mclstrpeakpics

annotate w4mclstrpeakpics.xml @ 0:caf0ce49b638 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
author eschen42
date Sun, 18 Jun 2017 23:25:58 -0400
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children 17356c5fe43e
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caf0ce49b638 planemo upload for repository https://github.com/HegemanLab/w4mclstrpeakpics_galaxy_wrapper/tree/master commit 7ff527179eab946dd860be6b6a3e2c01b77d7dee
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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="3.3.1">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="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 </requirements>
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10
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11 <stdio>
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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16 <command detect_errors="exit_code"><![CDATA[
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17 Rscript $__tool_directory__/w4mclstrpeakpics_wrapper.R
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18 data_matrix_path '$dataMatrix_in'
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19 variable_metadata_path '$variableMetadata_in'
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20 sample_metadata_path '$sampleMetadata_in'
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21 sample_selector_column_name '$sampleSelectorColumnName'
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22 sample_selector_value '$sampleSelectorValue'
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23 output_pdf '$outputFigure'
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24 output_tsv '$outputTable'
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25 output_rdata '$outputRdata'
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26 r_package_archive $__tool_directory__/w4mclstrpeakpics_0.98.1.tar.gz
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27 ; echo exit code $?
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28 ]]></command>
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30 <inputs>
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31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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32 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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33 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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34 <param name="sampleSelectorColumnName" label="Selector-column name" type="text" value = "sampleType" help="Name of column containing selector values." />
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35 <param name="sampleSelectorValue" label="Selector value" type="text" value = "pool" help="Value to match in sample-selector column." />
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36 </inputs>
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37 <outputs>
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38 <data name="outputTable" label="${tool.name}_${sampleSelectorValue}_table" format="tabular" ></data>
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39 <data name="outputFigure" label="${tool.name}_${sampleSelectorValue}_figure" format="pdf" ></data>
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40 <data name="outputRdata" label="${tool.name}_${sampleSelectorValue}_RData" format="rdata" ></data>
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41 </outputs>
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42
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43 <tests>
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44 <test>
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45 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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46 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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47 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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48 <param name="sampleSelectorColumnName" value="sampleType"/>
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49 <param name="sampleSelectorValue" value="pool"/>
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50 <output name="outputTable">
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51 <assert_contents>
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52 <has_text text="0.464572" />
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53 <has_text text="0.114304" />
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54 <has_text text="0.131016" />
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55 <has_text text="0.0701871" />
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56 <has_text text="0.0661764" />
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57 <has_text text="0.0384358" />
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58 <has_text text="0.0614973" />
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59 <has_text text="0.0260695" />
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60 <has_text text="0.0193850" />
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61 <has_text text="0.00835561" />
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66
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69 <help>
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70 <![CDATA[
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72 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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74 --------------------------------------------------------------------------
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77 **R package**
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79 The *w4mclstrpeakpics* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclstrpeakpics/releases).
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81 -----------------------------------------------------------------------------------------------------------------------------------------
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83
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84 **Tool updates**
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85
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86 See the **NEWS** section at the bottom of this page
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87
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88 ---------------------------------------------------
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89
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90 ==================================
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91 Visualize W4M sample-cluster peaks
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92 ==================================
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93
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94 -----------
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95 Description
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96 -----------
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97
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98 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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99
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100 -----------------
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101 Workflow Position
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102 -----------------
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103
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104 - Upstream tool category: Preprocessing
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105 - Downstream tool categories: (Not applicable.)
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106
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107 ----------
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108 Motivation
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109 ----------
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110
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111 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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112 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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113 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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114 However, the chromatographic retention time for a chemical can vary from one run to another.
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115 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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116
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117 In a typical GC-MS or LC-MS experiment, a pooled sample is repeatedly injected for quality control.
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118 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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119 However, the parameters for peak-picking can exacerbate injection-to-injection variation in performance of the experimental apparatus.
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120 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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121
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122 -----------
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123 Input files
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124 -----------
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125
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126 +---------------------------+------------+
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127 | File | Format |
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128 +===========================+============+
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129 | Data matrix | tabular |
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130 +---------------------------+------------+
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131 | Sample metadata | tabular |
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132 +---------------------------+------------+
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133 | Variable metadata | tabular |
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134 +---------------------------+------------+
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135
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136
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137 ----------
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138 Parameters
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139 ----------
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140
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141 Data matrix file
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142 | 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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143 |
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144
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145 Sample metadata file
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146 | 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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147 |
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148
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149 Variable metadata file
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150 | 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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151 |
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152
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153 Selector-column name (default = "sampleType")
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154 | column of W4M/XCMS sampleMetadata holding selector string values.
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155 |
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156
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157 Selector value (default = "pool")
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158 | value within selector column to identify samples for assessment.
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159 |
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160
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161 Include named classes (default = filter-out)
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162 | *filter-in* - include only the named sample classes
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163 | *filter-out* - exclude only the named sample classes
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164 |
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165
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166
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167 Column that names the sample-class (default = 'class')
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168 | name of the column in sample metadata that has the values to be tested against the 'classes' input parameter
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169 |
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170
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171 Column that names the sample (default = 'sampleMetadata')
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172 | name of the column in sample metadata that has the name of the sample
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173 |
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174
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175
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176 ------------
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177 Output files
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178 ------------
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179
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180
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181 View Cluster_Peaks_<SelectorName>_figure
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182 | (PDF) the output figure, described below.
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183 |
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184
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185 View Cluster_Peaks_<SelectorName>_table
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186 | (tabular separated values) table of the values plotted in the upper-left graph in the output figure.
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187 |
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188
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189 View Cluster_Peaks_<SelectorName>_rdata
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190 | (R data) RData containing all processing and plotting intermediates..
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191 |
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192
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193
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194 ------
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195 Graphs
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196 ------
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197
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198
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199 **The "Feature Number and Likelihood" graph**
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200
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201 The upper left graph in the output figure shows the following:
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202
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203 * 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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204 * 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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205 * 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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206
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207 .. 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)}
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208
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209 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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210
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211
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212 **The "Peak Intensity" graph**
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213
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214 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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215
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216 * 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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217 * 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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218
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219 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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220
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221
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222 **The "Symbol area/intensity reflect ion intensity" graph**
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223
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224 The upper right graph in the output figure shows the following:
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225
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226 * The X axis reflects the corrected retention time for each feature shown.
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227 * The Y axis reflects the m/z for each feature shown.
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228 * Symbol area reflects intensity for a feature for one sample.
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229 * 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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230 * 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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231
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232 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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233
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234
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235 **The "Symbol size/shape reflects prevalence" graph**
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236
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237 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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238
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239 * The X axis reflects the corrected retention time for each feature shown.
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240 * The Y axis reflects the m/z for each feature shown.
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241 * Symbol size and shape reflect the prevalence of a feature among the samples.
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242 * “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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243
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244 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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245
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246
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247 ---------------
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248 Working example
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249 ---------------
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250
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251 **Input files**
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252
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253 +-------------------+----------------------------------------------------------------------------------------------------------------+
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254 | Input File | Download from URL |
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255 +===================+================================================================================================================+
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256 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_dataMatrix.tsv |
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257 +-------------------+----------------------------------------------------------------------------------------------------------------+
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258 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_sampleMetadata.tsv |
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259 +-------------------+----------------------------------------------------------------------------------------------------------------+
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260 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclstrpeakpics/master/tests/testthat/input_variableMetadata.tsv |
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261 +-------------------+----------------------------------------------------------------------------------------------------------------+
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262
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263 **Other input parameters**
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264
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265 +------------------------------------+-----------------+
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266 | Input Parameter | Value |
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267 +====================================+=================+
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268 | Selector-column name | sampleType |
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269 +------------------------------------+-----------------+
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270 | Selector value | pool |
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271 +------------------------------------+-----------------+
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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 </help>
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277 <citations>
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278 <citation type="doi">10.1021/ac051437y</citation>
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279 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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280 </citations>
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281 <!--
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282 vim:noet:sw=4:ts=4
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283 --> </tool>