Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 27:30410a052ab3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
author lecorguille
date Tue, 24 Oct 2017 11:47:49 -0400
parents 411d2b9ea412
children 13885e67b123
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1 <tool id="abims_xcms_retcor" name="xcms.retcor" version="2.2.0">
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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
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19 method $methods.method
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20 #if $methods.method == "obiwarp":
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21 profStep $methods.profStep
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22 #else
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23 smooth $methods.smooth
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24 extra $methods.extra
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25 missing $methods.missing
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26 #if $methods.options.option == "show":
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27 span $methods.options.span
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28 family $methods.options.family
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29 plottype $methods.options.plottype
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30 #end if
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31 #end if
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33 @COMMAND_FILE_LOAD@
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35 @COMMAND_LOG_EXIT@
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36 ]]></command>
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37
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38 <inputs>
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39 <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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40 <conditional name="methods">
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41 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
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42 <option value="obiwarp" >obiwarp</option>
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43 <option value="peakgroups" selected="true">peakgroups</option>
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44 </param>
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45 <when value="obiwarp">
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46 <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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47 </when>
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48 <when value="peakgroups">
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49 <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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50 <option value="loess">loess</option>
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51 <option value="linear">linear</option>
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52 </param>
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53 <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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54 <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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55
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56 <conditional name="options">
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57 <param name="option" type="select" label="Advanced options">
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58 <option value="show">show</option>
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59 <option value="hide" selected="true">hide</option>
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60 </param>
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61 <when value="show">
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62 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
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63
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64 <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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65 <option value="gaussian" selected="true">gaussian</option>
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66 <option value="symmetric">symmetric</option>
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67 </param>
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68
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69 <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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70 <option value="none" selected="true">none</option>
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71 <option value="deviation">deviation</option>
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72 <option value="mdevden">mdevden</option>
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73 </param>
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74
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75 </when>
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76 <when value="hide">
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77 </when>
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78 </conditional>
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79 </when>
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80 </conditional>
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82 <expand macro="input_file_load"/>
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83 <expand macro="input_tic_bpc_pdf"/>
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84
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85 </inputs>
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86
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87 <outputs>
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88 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" />
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89 <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.retcor.Rplots.pdf">
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90 <filter>(methods['method'] == 'peakgroups')</filter>
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91 <filter>(methods['options']['option'] == 'show')</filter>
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92 <filter>(methods['options']['family'] == 'symmetric')</filter>
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93 <filter>(methods['options']['plottype'] != 'none')</filter>
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94 </data>
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95 <data name="ticsCorPdf" format="pdf" from_work_dir="TICs.pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf">
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96 <filter>tic_bpc_pdf</filter>
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97 </data>
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98 <data name="bpcsCorPdf" format="pdf" from_work_dir="BPCs.pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf">
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99 <filter>tic_bpc_pdf</filter>
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100 </data>
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101 <collection name="ticsCorrectedTabCollection" type="list" label="TIC corrected tabular">
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102 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
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103 <discover_datasets pattern="(?P&lt;designation&gt;.+)-TIC_corrected_mqc\.out" ext="tabular" visible="true" />
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104 </collection>
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105 <collection name="bpcsCorrectedTabCollection" type="list" label="BPC corrected tabular">
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106 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
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107 <discover_datasets pattern="(?P&lt;designation&gt;.+)-BPC_corrected_mqc\.out" ext="tabular" visible="true" />
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108 </collection>
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109 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
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110 </outputs>
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111
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112 <tests>
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113 <!--<test>
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114 <param name="image" value="xset.group.RData"/>
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115 <param name="methods|method" value="peakgroups"/>
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116 <param name="methods|smooth" value="loess"/>
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117 <param name="methods|extra" value="1"/>
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118 <param name="methods|missing" value="1"/>
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119 <param name="methods|options|option" value="show"/>
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120 <param name="methods|options|span" value="0.2"/>
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121 <param name="methods|options|family" value="gaussian"/>
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122 <param name="methods|options|plottype" value="deviation"/>
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123 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
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124 <param name="zipfile_load_conditional|zip_file" value="sacuri_dir_root.zip" ftype="zip" />
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125 <output name="log">
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126 <assert_contents>
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127 <has_text text="object with 4 samples" />
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128 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
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129 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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130 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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131 <has_text text="Peak Groups: 0" />
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132 <has_text text="Sample classes: bio, blank" />
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133 </assert_contents>
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134 </output>
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135 </test>-->
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136 <test>
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137 <param name="image" value="faahKO.xset.group.RData"/>
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138 <expand macro="test_retcor_param"/>
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139 <expand macro="test_file_load_zip"/>
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140 <expand macro="test_retcor_output" raworcorrected="_corrected" />
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141 </test>
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142 <test>
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143 <param name="image" value="faahKO-single-class.xset.group.RData"/>
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144 <expand macro="test_retcor_param" />
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145 <expand macro="test_file_load_single"/>
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146 <expand macro="test_retcor_output" raworcorrected="_corrected" />
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147 </test>
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148 </tests>
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149
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150 <help><![CDATA[
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151
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152 @HELP_AUTHORS@
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153
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154 ===========
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155 Xcms.retcor
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156 ===========
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157
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158 Description
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159 -----------
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160
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161 After matching peaks into groups, xcms can use those groups to identify and correct
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162 correlated drifts in retention time from run to run. The aligned peaks can then be
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163 used for a second pass of peak grouping which will be more accurate than the first.
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164 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
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165 for identifying retention time drifts. Some groups may be missing peaks from a large
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166 fraction of samples and thus provide an incomplete picture of the drift at that time point.
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167 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
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168
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169 .. class:: warningmark
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170
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171 **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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172 discarded)**
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173
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174
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175
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176 Workflow position
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177 -----------------
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178
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179
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180 **Upstream tools**
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181
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182 +------------------------+------------------+--------------------+------------+
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183 | Name | output file | format | parameter |
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184 +========================+==================+====================+============+
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185 | xcms.group | xset.group.RData | RData | RData file |
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186 +------------------------+------------------+--------------------+------------+
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187
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188
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189 **Downstream tools**
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190
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191 +---------------------------+------------------+--------+
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192 | Name | Output file | Format |
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193 +===========================+==================+========+
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194 |xcms.group | xset.retcor.RData| RData |
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195 +---------------------------+------------------+--------+
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196
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197 **General schema of the metabolomic workflow**
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198
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199 .. image:: xcms_retcor_workflow.png
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200
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201
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202 ---------------------------------------------------
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203
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204 -----------
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205 Input files
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206 -----------
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207
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208 +---------------------------+----------------------+
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209 | Parameter : num + label | Format |
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210 +===========================+======================+
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211 | 1 : RData file | rdata.xcms.group |
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212 +---------------------------+----------------------+
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213
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214
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215 ----------
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216 Parameters
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217 ----------
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218
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219 Method
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220 ------
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221
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222 **peakgroups**
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223
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224 | 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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225 | 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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226 | However, it is possible to enable outlier detection and removal by setting the **family** argument to **symmetric**.
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227
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228 **obiwarp**
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229
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230 | 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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231 | 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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232
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233
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234 ------------
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235 Output files
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236 ------------
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237
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238 xset.group.retcor.RData: rdata.xcms.retcor format
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239
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240 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
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241
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242 @HELP_BCP_TIC@
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243
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244
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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 | RData file -> **xset.group.RData**
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255
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256 Parameters
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257 ----------
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258
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259 | **Method**: peakgroups
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260 | **smooth**: loess
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261 | **extra**: 1
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262 | **missing**: 5
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263 | **Advanced options**: show
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264 | **span**: 0.4
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265 | **family**: gaussian
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266 | **plottype**: deviation
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267
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268
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269 ---------------------------------------------------
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270
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271 Changelog/News
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272 --------------
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273
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274 **Version 2.2.0 - 19/10/2017**
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276 - NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC.
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277
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278 **Version 2.1.0 - 03/02/2017**
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280 - IMPROVEMENT: xcms.retcor can deal with merged individual data
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281
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282 **Version 2.0.8 - 22/12/2016**
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283
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284 - 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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285
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286 **Version 2.0.7 - 06/07/2016**
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287
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288 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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289
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290 **Version 2.0.6 - 04/04/2016**
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291
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292 - TEST: refactoring to pass planemo test using conda dependencies
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293
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294
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295 **Version 2.0.5 - 10/02/2016**
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296
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297 - BUGFIX: better management of errors. Datasets remained green although the process failed
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298
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299 - BUGFIX: some pdf remained empty even when the process succeed
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300
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301 - UPDATE: refactoring of internal management of inputs/outputs
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302
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303 - UPDATE: refactoring to feed the new report tool
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304
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305
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306 **Version 2.0.2 - 02/06/2015**
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307
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308 - 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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309
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310 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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311
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312
1
f42bd3de6aad Uploaded
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313 ]]></help>
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314
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315
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316 <expand macro="citation" />
0
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317
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318 </tool>