annotate abims_xcms_xcmsSet.xml @ 14:363cce459fff draft

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author lecorguille
date Tue, 13 Feb 2018 04:47:50 -0500
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1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1">
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2 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @COMMAND_XCMS_SCRIPT@
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14 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
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15 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
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16 #else
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17 zipfile '$input'
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18 #end if
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19
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20 xfunction xcmsSet
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21
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22 xsetRdataOutput '$xsetRData'
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23 sampleMetadataOutput '$sampleMetadata'
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24 ticspdf '$ticsRawPdf'
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25 bicspdf '$bpcsRawPdf'
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28 #if $options_scanrange.option == "show":
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29 scanrange "c($options_scanrange.scanrange)"
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30 #end if
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32 ## profmethod $profmethod
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33 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
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34 #if $methods.method == "centWave":
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35 ppm $methods.ppm
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36 peakwidth "c($methods.peakwidth)"
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37 #if $methods.options_c.option == "show":
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38 mzdiff $methods.options_c.mzdiff
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39 snthresh $methods.options_c.snthresh
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40 integrate $methods.options_c.integrate
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41 noise $methods.options_c.noise
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42 prefilter "c($methods.options_c.prefilter)"
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43 #end if
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44 #elif $methods.method == "matchedFilter":
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45 step $methods.step
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46 fwhm $methods.fwhm
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47 #if $methods.options_m.option == "show":
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48 ## sigma "$methods.options_m.sigma"
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49 max $methods.options_m.max
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50 snthresh $methods.options_m.snthresh
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51 steps $methods.options_m.steps
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52 mzdiff $methods.options_m.mzdiff
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53 #end if
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54 #elif $methods.method == "MSW":
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55 snthr $methods.snthr
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56 nearbyPeak $methods.nearbyPeak
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57 winSize.noise $methods.winSize_noise
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58 amp.Th $methods.amp_Th
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59 scales "c($methods.scales)"
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60 SNR.method "$methods.SNR_method"
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61 #end if
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62 @COMMAND_LOG_EXIT@
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63 ]]></command>
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64
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65 <inputs>
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66
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67 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
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68
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69 <conditional name="options_scanrange">
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70 <param name="option" type="select" label="Scan range option " >
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71 <option value="show">show</option>
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72 <option value="hide" selected="true">hide</option>
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73 </param>
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74 <when value="show">
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75 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
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76 <validator type="empty_field"/>
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77 </param>
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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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83
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84 <!--
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85 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
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86 <option value="bin" selected="true">bin</option>
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87 <option value="binlin">binlin</option>
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88 <option value="binlinbase">binlinbase</option>
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89 <option value="intlin">intlin</option>
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90 </param>
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91 -->
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92 <conditional name="methods">
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93 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
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94 <option value="centWave" >centWave</option>
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95 <option value="matchedFilter" selected="true">matchedFilter</option>
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96 <option value="MSW">MSW</option>
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97 </param>
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98
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99 <!-- centWave Filter options -->
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100 <when value="centWave">
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101 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
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102 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
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103
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104 <conditional name="options_c">
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105 <param name="option" type="select" label="Advanced options" >
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106 <option value="show">show</option>
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107 <option value="hide" selected="true">hide</option>
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108 </param>
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109 <when value="show">
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110 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
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111 <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap" />
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112 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
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113 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
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114 <option value="2">peak limits based on real data (more sensitive to noise)</option>
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115 </param>
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116 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
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117 <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
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118 </when>
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119 <when value="hide">
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120 </when>
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121 </conditional>
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122 </when>
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123
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124 <!-- matched Filter options -->
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125 <when value="matchedFilter">
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126 <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
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127 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
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128 <conditional name="options_m">
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129 <param name="option" type="select" label="Advanced options" >
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130 <option value="show">show</option>
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131 <option value="hide" selected="true">hide</option>
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132 </param>
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133 <when value="show">
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134 <!--<param name="sigma" type="float" value="12.739935451" label="Standard deviation (width) of matched filtration model peak" help="[sigma] By default: fwhm/2.3548" />-->
0
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135 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
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136 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
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137 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
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138 <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " />
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139 </when>
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140 <when value="hide">
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141 </when>
0
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142 </conditional>
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143 </when>
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144
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145 <!-- MSW Filter options -->
0
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146 <when value="MSW">
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147 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
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148 <option value="TRUE">TRUE</option>
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149 <option value="FALSE">FALSE</option>
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150 </param>
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151 <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />
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152 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
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153 <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
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154 <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
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155 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
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156 </when>
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157 </conditional>
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158 </inputs>
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159
0
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160 <outputs>
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161 <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
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162 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
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163 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
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164 </data>
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165 <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
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166 <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
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167 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
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168 </outputs>
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169
0
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170 <tests>
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171 <!--<test>
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172 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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173 <param name="methods|method" value="matchedFilter" />
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174 <param name="methods|step" value="0.01" />
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175 <param name="methods|fwhm" value="4" />
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176 <param name="methods|options_m|option" value="show" />
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177 <param name="methods|options_m|max" value="50" />
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178 <param name="methods|options_m|snthresh" value="1" />
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179 <param name="methods|options_m|steps" value="2" />
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180 <output name="log">
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181 <assert_contents>
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182 <has_text text="object with 4 samples" />
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183 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
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184 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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185 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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186 <has_text text="Peak Groups: 0" />
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187 <has_text text="Sample classes: bio, blank" />
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188 </assert_contents>
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189 </output>
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190 </test>
6
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191 <test>
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192 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
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193 <param name="methods|method" value="centWave" />
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194 <param name="methods|ppm" value="25" />
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195 <param name="methods|peakwidth" value="20,50" />
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196 <output name="log">
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197 <assert_contents>
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198 <has_text text="object with 4 samples" />
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199 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
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200 <has_text text="Mass range: 57.9756-593.4086 m/z" />
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201 <has_text text="Peaks: 1535 (about 384 per sample)" />
5
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202 <has_text text="Peak Groups: 0" />
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203 <has_text text="Sample classes: bio, blank" />
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204 </assert_contents>
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205 </output>
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206 </test>-->
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207 <test>
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208 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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209 <param name="methods|method" value="centWave" />
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210 <param name="methods|ppm" value="25" />
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211 <param name="methods|peakwidth" value="20,50" />
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212 <output name="log">
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213 <assert_contents>
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214 <has_text text="object with 4 samples" />
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215 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
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216 <has_text text="Mass range: 200.1-600 m/z" />
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217 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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218 <has_text text="Peak Groups: 0" />
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219 <has_text text="Sample classes: KO, WT" />
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220 </assert_contents>
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221 </output>
0
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222 </test>
12
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223 <!-- Passed but disable to save time for Travis" -->
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224 <!--<test>
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225 <param name="input" value="ko15.CDF" ftype="netcdf" />
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226 <param name="methods|method" value="centWave" />
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227 <param name="methods|ppm" value="25" />
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228 <param name="methods|peakwidth" value="20,50" />
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229 <output name="log">
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230 <assert_contents>
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231 <has_text text="object with 1 samples" />
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232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
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diff changeset
233 <has_text text="Mass range: 200.2-600 m/z" />
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234 <has_text text="Peaks: 2262 (about 2262 per sample)" />
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parents: 11
diff changeset
235 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
236 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
237 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
238 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
239 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
240 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
241 <param name="input" value="ko16.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
242 <param name="methods|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
243 <param name="methods|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
244 <param name="methods|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
245 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
246 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
247 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
248 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
249 <has_text text="Mass range: 200.1-600 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
250 <has_text text="Peaks: 2408 (about 2408 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
251 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
252 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
253 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
254 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
255 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
256 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
257 <param name="input" value="wt15.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
258 <param name="methods|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
259 <param name="methods|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
260 <param name="methods|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
261 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
262 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
263 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
264 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
265 <has_text text="Mass range: 200.2-599.8 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
266 <has_text text="Peaks: 2278 (about 2278 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
267 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
268 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
269 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
270 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
271 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
272 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
273 <param name="inputs|input" value="single_file" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
274 <param name="inputs|single_file" value="wt16.CDF" ftype="netcdf" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
275 <param name="methods|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
276 <param name="methods|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
277 <param name="methods|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
278 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
279 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
280 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
281 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
282 <has_text text="Mass range: 200.3-600 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
283 <has_text text="Peaks: 2303 (about 2303 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
284 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
285 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
286 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
287 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
288 </test>-->
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
289 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
290 <param name="input" value="HU_neg_017.mzXML" ftype="mzxml" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
291 <param name="methods|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
292 <param name="methods|ppm" value="25" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
293 <param name="methods|peakwidth" value="20,50" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
294 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
295 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
296 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
297 <has_text text="Time range: 3.5-1139.1 seconds (0.1-19 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
298 <has_text text="Mass range: 57.9756-556.8128 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
299 <has_text text="Peaks: 380 (about 380 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
300 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
301 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
302 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
303 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
304 </test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
305 <test>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
306 <param name="input" value="MM14.mzML" ftype="mzxml" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
307 <param name="methods|method" value="centWave" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
308 <param name="methods|ppm" value="56" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
309 <param name="methods|peakwidth" value="5.275,13.5" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
310 <output name="log">
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
311 <assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
312 <has_text text="object with 1 samples" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
313 <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
314 <has_text text="Mass range: 117.0357-936.7059 m/z" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
315 <has_text text="Peaks: 222 (about 222 per sample)" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
316 <has_text text="Peak Groups: 0" />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
317 <has_text text="Sample classes: ." />
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
318 </assert_contents>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
319 </output>
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
320 </test>
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
321 </tests>
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
322
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
323 <help><![CDATA[
0
054e4681667c planemo upload
lecorguille
parents:
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324
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
325 @HELP_AUTHORS@
0
054e4681667c planemo upload
lecorguille
parents:
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326
054e4681667c planemo upload
lecorguille
parents:
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327 ============
054e4681667c planemo upload
lecorguille
parents:
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328 Xcms.xcmsSet
054e4681667c planemo upload
lecorguille
parents:
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329 ============
054e4681667c planemo upload
lecorguille
parents:
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330
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lecorguille
parents:
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331 -----------
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lecorguille
parents:
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332 Description
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lecorguille
parents:
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333 -----------
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lecorguille
parents:
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334
054e4681667c planemo upload
lecorguille
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335 This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
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336 You can read a tutorial on how to perform xcms preprocessing which is available here_.
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337
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338 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
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339
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340
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341 -----------------
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342 Workflow position
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343 -----------------
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344
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345 **Upstream tools**
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346
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347 ========================= ================= ======= =========
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348 Name output file format parameter
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349 ========================= ================= ======= =========
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350 NA NA zip NA
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351 ========================= ================= ======= =========
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352
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353
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354 **Downstream tools**
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355
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356 +---------------------------+--------------------+-----------------+
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357 | Name | Output file | Format |
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358 +===========================+====================+=================+
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359 |xcms.group | xset.RData | rdata.xcms.raw |
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360 +---------------------------+--------------------+-----------------+
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361 |PCA ellipsoid by factors | sampleMetadata.tsv | Tabular |
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362 +---------------------------+--------------------+-----------------+
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363 |Anova | sampleMetadata.tsv | Tabular |
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364 +---------------------------+--------------------+-----------------+
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365
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366
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367 **Example of a metabolomic workflow**
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368
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369 .. image:: xcms_xcmsset_workflow.png
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370
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371
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372 ------
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373
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374 .. class:: infomark
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375
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376 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
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377
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378 ---------------------------------------------------
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379
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380
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381
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382 -----------
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383 Input files
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384 -----------
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385
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386 +---------------------------+----------------------------------+
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387 | Parameter : num + label | Format |
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388 +===========================+==================================+
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389 | OR : Zip file | zip |
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390 +---------------------------+----------------------------------+
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391 | OR : Single file | mzXML, mzML, mzData, netCDF |
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392 +---------------------------+----------------------------------+
0
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393
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394 **Choose your inputs**
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395
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396 You have two methods for your inputs:
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397
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398 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
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399 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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400
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401 Zip file: Steps for creating the zip file
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402 -----------------------------------------
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403
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404 **Step1: Creating your directory and hierarchize the subdirectories**
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405
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406
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407 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip software (http://www.7-zip.org/), otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
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408
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409 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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410 arabidopsis/wild/01.raw
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411 arabidopsis/mutant/01.raw
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412
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413 **Step2: Creating a zip file**
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414
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415 Create your zip file (e.g.: arabidopsis.zip).
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416
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417 **Step 3 : Uploading it to our Galaxy server**
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418
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419 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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420
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421 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO on workflow4metabolomics.org (http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf).
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422
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423 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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424
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425 Advices for converting your files for the XCMS input
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426 ----------------------------------------------------
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427
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428 We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
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429
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430 **We recommend you the following parameters:**
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431
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432 Use Filtering: **True**
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433
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434 Use Peak Picking: **True**
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435
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436 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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437
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438 Use zlib: **64**
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439
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440 Binary Encoding: **64**
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441
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442 m/z Encoding: **64**
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443
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444 Intensity Encoding: **64**
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445
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446
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447 ----------
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448 Parameters
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449 ----------
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450
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451 Extraction method for peaks detection
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452 -------------------------------------
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453
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454 **Matched Filter**
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455
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456 | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
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457 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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458
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459
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460 **cent Wave**
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461
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462 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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463 | Due to the fact that peak centroids are used, a binning step is not necessary.
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464 | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
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465
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466 **MSW**
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467
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468 | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
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469 | If you wish to have more details about the other parameters, you can read the following documents:
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470 | -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf
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471 | -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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472
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473
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474 ------------
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475 Output files
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476 ------------
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477
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478 xset.TICs_raw.pdf
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479
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480 | "Total Ion Chromatograms" graph in pdf format.
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481
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482 xset.BPCs_raw.pdf
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483
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484 | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
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485
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486 sampleMetadata.tsv
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487
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488 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
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489 | This file is necessary in the Anova and PCA step of the workflow.
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490
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491 xset.RData: rdata.xcms.raw format
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492
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493 | Rdata file that is necessary in the second step of the workflow "xcms.group".
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494
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495 ------
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496
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497 .. class:: infomark
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498
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499 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
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500
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501 ---------------------------------------------------
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502
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503 ---------------
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504 Working example
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505 ---------------
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506
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507 Input files
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508 -----------
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509
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510 | zip_file -> **sacuri.zip**
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511
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512 Parameters
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513 ----------
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514
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515 | Method -> **matchedFilter**
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516 | step -> **0.01**
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517 | fwhm -> **4**
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518 | Advanced option -> **show**
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519 | max: -> **50**
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520 | snthresh -> **1**
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521 | steps -> **2**
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522
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523
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524 Output files
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525 ------------
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526
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527 | **1) xset.RData: RData file**
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528
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529 | **2) Example of a sampleMetadata.tsv :**
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530
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531
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532 +---------------------------+------------+---------+
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533 | sampleMetadata | class | polarity|
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534 +===========================+============+=========+
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535 |HU_neg_017 | bio |negative |
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536 +---------------------------+------------+---------+
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537 |HU_neg_028 | bio |negative |
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538 +---------------------------+------------+---------+
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539 |HU_neg_034 | bio |negative |
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540 +---------------------------+------------+---------+
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541 |Blanc04 | blank |negative |
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542 +---------------------------+------------+---------+
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543 |Blanc06 | blank |negative |
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544 +---------------------------+------------+---------+
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545 |Blanc09 | blank |negative |
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546 +---------------------------+------------+---------+
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547
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548
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549
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550 | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**
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551
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552 .. image:: xcms_tics.png
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553
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554
5
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555 ---------------------------------------------------
4
c5fa73f1703f Uploaded
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556
5
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557 Changelog/News
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558 --------------
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559
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
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560 **Version 2.1.1 - 29/11/2017**
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561
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562 - 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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563
12
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564 **Version 2.1.0 - 22/02/2017**
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565
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566 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
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567
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568 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
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569
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570 **Version 2.0.11 - 22/12/2016**
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571
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572 - BUGFIX: propose scanrange for all methods
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573
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574 **Version 2.0.10 - 22/12/2016**
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575
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576 - 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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577
10
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578 **Version 2.0.9 - 06/07/2016**
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579
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580 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
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581
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582 **Version 2.0.8 - 06/04/2016**
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583
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584 - TEST: refactoring to pass planemo test using conda dependencies
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585
5
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586
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587 **Version 2.0.7 - 10/02/2016**
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588
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589 - BUGFIX: better management of errors. Datasets remained green although the process failed
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590
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591 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
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592
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593 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
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594
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595 - UPDATE: refactoring of internal management of inputs/outputs
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596
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597 - TEST: refactoring to feed the new report tool
5
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598
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599
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600 **Version 2.0.2 - 18/01/2016**
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601
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602 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
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603
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604
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605 **Version 2.0.2 - 09/10/2015**
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606
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607 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
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608
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609
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610 **Version 2.0.2 - 02/06/2015**
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611
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612 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
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613
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614 - 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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615
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616 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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617
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618 ]]></help>
0
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619
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620 <expand macro="citation" />
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621 </tool>