Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 29:c013ed353a2f draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
author lecorguille
date Tue, 13 Feb 2018 04:44:03 -0500
parents 13885e67b123
children 4d6f4cd7c3ef
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1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.1">
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2
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3 <description>Retention Time Correction using retcor function from xcms R package </description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_XCMS_SCRIPT@
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14 image '$image'
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15 xfunction retcor
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17 xsetRdataOutput '$xsetRData'
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18 ticspdf '$ticsCorPdf'
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19 bicspdf '$bpcsCorPdf'
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20 rplotspdf '$rplotsPdf'
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21
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22 method $methods.method
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23 #if $methods.method == "obiwarp":
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24 profStep $methods.profStep
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25 #else
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26 smooth $methods.smooth
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27 extra $methods.extra
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28 missing $methods.missing
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29 #if $methods.options.option == "show":
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30 span $methods.options.span
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31 family $methods.options.family
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32 plottype $methods.options.plottype
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33 #end if
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34 #end if
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36 @COMMAND_FILE_LOAD@
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38 @COMMAND_LOG_EXIT@
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39 ]]></command>
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40
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41 <inputs>
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42 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
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43 <conditional name="methods">
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44 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
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45 <option value="obiwarp" >obiwarp</option>
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46 <option value="peakgroups" selected="true">peakgroups</option>
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47 </param>
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48 <when value="obiwarp">
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49 <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" />
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50 </when>
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51 <when value="peakgroups">
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52 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
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53 <option value="loess">loess</option>
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54 <option value="linear">linear</option>
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55 </param>
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56 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
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57 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
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58
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59 <conditional name="options">
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60 <param name="option" type="select" label="Advanced options">
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61 <option value="show">show</option>
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62 <option value="hide" selected="true">hide</option>
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63 </param>
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64 <when value="show">
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65 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
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66
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67 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
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68 <option value="gaussian" selected="true">gaussian</option>
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69 <option value="symmetric">symmetric</option>
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70 </param>
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71
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72 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
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73 <option value="none" selected="true">none</option>
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74 <option value="deviation">deviation</option>
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75 <option value="mdevden">mdevden</option>
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76 </param>
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77
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78 </when>
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79 <when value="hide">
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80 </when>
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81 </conditional>
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82 </when>
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83 </conditional>
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85 <expand macro="input_file_load"/>
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86
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87 </inputs>
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88
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89 <outputs>
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90 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
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91 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
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92 <filter>(methods['method'] == 'peakgroups')</filter>
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93 <filter>(options['option'] == 'show')</filter>
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94 <filter>(family == 'symmetric')</filter>
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95 <filter>(plottype != 'none')</filter>
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96 </data>
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97 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
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98 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
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99 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
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100 </outputs>
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101
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102 <tests>
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103 <!--<test>
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104 <param name="image" value="xset.group.RData"/>
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105 <param name="methods|method" value="peakgroups"/>
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106 <param name="methods|smooth" value="loess"/>
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107 <param name="methods|extra" value="1"/>
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108 <param name="methods|missing" value="1"/>
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109 <param name="methods|options|option" value="show"/>
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110 <param name="methods|options|span" value="0.2"/>
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111 <param name="methods|options|family" value="gaussian"/>
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112 <param name="methods|options|plottype" value="deviation"/>
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113 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
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114 <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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115 <output name="log">
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116 <assert_contents>
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117 <has_text text="object with 4 samples" />
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118 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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119 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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120 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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121 <has_text text="Peak Groups: 0" />
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122 <has_text text="Sample classes: bio, blank" />
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123 </assert_contents>
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124 </output>
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125 </test>-->
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126 <test>
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127 <param name="image" value="faahKO.xset.group.RData"/>
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128 <param name="methods|method" value="peakgroups"/>
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129 <param name="methods|smooth" value="loess"/>
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130 <param name="methods|extra" value="1"/>
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131 <param name="methods|missing" value="1"/>
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132 <param name="methods|options|option" value="show"/>
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133 <param name="methods|options|span" value="0.2"/>
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134 <param name="methods|options|family" value="gaussian"/>
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135 <param name="methods|options|plottype" value="deviation"/>
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136 <expand macro="test_file_load_zip"/>
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137 <output name="log">
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138 <assert_contents>
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139 <has_text text="object with 4 samples" />
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140 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
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141 <has_text text="Mass range: 200.1-600 m/z" />
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142 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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143 <has_text text="Peak Groups: 0" />
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144 <has_text text="Sample classes: KO, WT" />
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145 </assert_contents>
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146 </output>
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147 </test>
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148 <test>
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149 <param name="image" value="faahKO-single-class.xset.group.RData"/>
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150 <param name="methods|method" value="peakgroups"/>
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151 <param name="methods|smooth" value="loess"/>
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152 <param name="methods|extra" value="1"/>
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153 <param name="methods|missing" value="1"/>
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154 <param name="methods|options|option" value="show"/>
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155 <param name="methods|options|span" value="0.2"/>
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156 <param name="methods|options|family" value="gaussian"/>
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157 <param name="methods|options|plottype" value="deviation"/>
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158 <expand macro="test_file_load_single"/>
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159 <output name="log">
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160 <assert_contents>
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161 <has_text text="object with 4 samples" />
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162 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
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163 <has_text text="Mass range: 200.1-600 m/z" />
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164 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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165 <has_text text="Peak Groups: 0" />
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166 <has_text text="Sample classes: KO, WT" />
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167 </assert_contents>
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168 </output>
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169 </test>
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170 </tests>
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171
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f42bd3de6aad Uploaded
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172 <help><![CDATA[
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173
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174 @HELP_AUTHORS@
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175
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176 ===========
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177 Xcms.retcor
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178 ===========
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179
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180 -----------
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181 Description
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182 -----------
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183
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184 After matching peaks into groups, xcms can use those groups to identify and correct
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185 correlated drifts in retention time from run to run. The aligned peaks can then be
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186 used for a second pass of peak grouping which will be more accurate than the first.
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187 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
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188 for identifying retention time drifts. Some groups may be missing peaks from a large
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189 fraction of samples and thus provide an incomplete picture of the drift at that time point.
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190 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
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191
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192 .. class:: warningmark
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193
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194 **After an retcor step, it is mandatory to do a group step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
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195 discarded)**
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196
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197
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198
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199 -----------------
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200 Workflow position
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201 -----------------
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202
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203
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204 **Upstream tools**
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205
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206 ========================= ================= ======= ==========
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207 Name output file format parameter
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208 ========================= ================= ======= ==========
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209 xcms.group xset.group.RData RData RData file
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210 ========================= ================= ======= ==========
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211
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212
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213 **Downstream tools**
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214
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215 +---------------------------+------------------+--------+
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216 | Name | Output file | Format |
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217 +===========================+==================+========+
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218 |xcms.group | xset.retcor.RData| RData |
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219 +---------------------------+------------------+--------+
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220
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221 The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
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222
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223
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224 **General schema of the metabolomic workflow**
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225
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226 .. image:: xcms_retcor_workflow.png
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227
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228
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229 -----------
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230 Input files
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231 -----------
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232
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233 +---------------------------+----------------------+
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234 | Parameter : num + label | Format |
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235 +===========================+======================+
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236 | 1 : RData file | rdata.xcms.group |
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237 +---------------------------+----------------------+
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238
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239
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240 ----------
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241 Parameters
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242 ----------
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243
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244 Method
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245 ------
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246
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247 **peakgroups**
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248
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249 | xcms ignores those groups by only considering well-behaved peak groups which are missing at most one sample and have at most one extra peak. (Those values can be changed with the **missing** and **extra** arguments.)
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250 | For each of those well-behaved groups, the algorithm calculates a median retention time and, for every sample, a deviation from that median. Within a sample, the observed deviation generally changes over time in a nonlinear fashion. Those changes are approximated using a local polynomial regression technique implemented in the **loess** function. By default, the curve fitting is done using least-squares on all data points.
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251 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**.
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252
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253 **obiwarp**
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254
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255 | Calculate retention time deviations for each sample using the obiwarp code at "http://obi-warp.sourceforge.net/". This function is able to align multiple samples by a center-star strategy. Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function. OBI-Warp harnesses the non-linear, comprehensive alignment power of DTW and builds on the discrete, non-bijective output of DTW to give natural interpolants that can be used across multiple datasets.
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256 | For the original publication see :**Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpo-lated Warping John T. Prince and, Edward M. Marcotte Analytical Chemistry 2006 78 (17), 6140-6152.**
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257
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258
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259 ------------
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260 Output files
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261 ------------
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262
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263 xset.group.retcor.TICs_corrected.pdf
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265 | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
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267 xset.group.retcor.BPCs_corrected.pdf
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269 | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
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270
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271 xset.group.retcor.RData: rdata.xcms.retcor format
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272
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273 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
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274
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276 ------
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278 .. class:: infomark
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280 The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
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281
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282
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283 ---------------------------------------------------
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284
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285 ---------------
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286 Working example
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287 ---------------
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288
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289 Input files
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290 -----------
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291
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292 | RData file -> **xset.group.RData**
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293
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294 Parameters
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295 ----------
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296
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297 | Method: -> **peakgroups**
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298 | smooth: -> **loess**
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299 | extra: -> **1**
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300 | missing -> **1**
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301 | Advanced options: -> **show**
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302 | span -> **0.2**
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303 | family -> **gaussian**
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304 | plottype -> **deviation**
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307 Output files
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308 ------------
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310 | **1) xset.group.retcor.RData: RData file**
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311
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312 | **2) Example of an xset.group.retcor.TICs_corrected pdf file**
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314 .. image:: xcms_retcor.png
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315
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316
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317 ---------------------------------------------------
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318
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319 Changelog/News
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320 --------------
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321
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322 **Version 2.1.1 - 29/11/2017**
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323
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324 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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325
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326 **Version 2.1.0 - 03/02/2017**
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327
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328 - IMPROVEMENT: xcms.retcor can deal with merged individual data
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329
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330 **Version 2.0.8 - 22/12/2016**
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331
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332 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
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333
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334 **Version 2.0.7 - 06/07/2016**
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335
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336 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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337
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338 **Version 2.0.6 - 04/04/2016**
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339
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340 - TEST: refactoring to pass planemo test using conda dependencies
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341
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342
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343 **Version 2.0.5 - 10/02/2016**
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344
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345 - BUGFIX: better management of errors. Datasets remained green although the process failed
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346
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347 - BUGFIX: some pdf remained empty even when the process succeed
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348
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349 - UPDATE: refactoring of internal management of inputs/outputs
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350
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351 - UPDATE: refactoring to feed the new report tool
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352
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353
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354 **Version 2.0.2 - 02/06/2015**
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355
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356 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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357
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358 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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359
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360
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361 ]]></help>
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362
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363
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364 <expand macro="citation" />
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365
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366 </tool>