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annotate ipo4xcmsSet.xml @ 7:dd0a593dded1 draft

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author lecorguille
date Wed, 12 Apr 2017 08:53:04 -0400
parents 03fdfbd914ab
children 364756ea5f42
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1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="0.0.3">
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3 <description>IPO optimization process for xcms.xcmsSet</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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8 <macro name="centwave_ppm_fixed">
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9 <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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10 </macro>
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11 <macro name="centwave_peakwidth_fixed">
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12 <param name="min_peakwidth" type="float" value="20" label="Min peak width range in seconds" optional="true" help="[min_peakwidth]" />
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13 <param name="max_peakwidth" type="float" value="50" label="Max peak width range in seconds" optional="true" help="[max_peakwidth]" />
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14 </macro>
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15 <macro name="centwave_mzdiff_fixed">
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16 <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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17 </macro>
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18
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19 <macro name="matchedfilter_fwhm_fixed">
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20 <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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21 </macro>
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22 <macro name="matchedfilter_mzdiff_fixed">
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23 <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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24 </macro>
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25 </macros>
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26
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27 <expand macro="requirements"/>
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28 <expand macro="stdio"/>
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29
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30 <command><![CDATA[
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31 LANG=C Rscript $__tool_directory__/ipo4xcmsSet.r
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32
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33 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
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34 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
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35 #else
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36 zipfile '$input'
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37 #end if
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38
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39 parametersOutput $parametersOutput
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40 xsetRdataOutput $xsetRData
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42 samplebyclass $samplebyclass
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43
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44 ## profmethod $profmethod
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45 @COMMAND_NSLAVES@
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46 method $methods.method
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47 #if $methods.method == "centWave":
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48 ppm "c($methods.section_centwave_optiomizable.conditional_parameter.ppm)"
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49 min_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.min_peakwidth)"
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50 max_peakwidth "c($methods.section_centwave_optiomizable.conditional_parameter.max_peakwidth)"
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51 mzdiff "c($methods.section_centwave_optiomizable.conditional_parameter.mzdiff)"
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52
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53 snthresh $methods.section_centwave_non_optiomizable.snthresh
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54 integrate $methods.section_centwave_non_optiomizable.integrate
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55 noise $methods.section_centwave_non_optiomizable.noise
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56 prefilter "c($methods.section_centwave_non_optiomizable.prefilter)"
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57
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58 #elif $methods.method == "matchedFilter":
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59 fwhm "c($methods.section_matchedfilter_optiomizable.conditional_parameter.fwhm)"
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60 mzdiff "c($methods.section_matchedfilter_optiomizable.conditional_parameter.mzdiff)"
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61
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62 step $methods.section_matchedfilter_non_optimizable.step
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63 steps $methods.section_matchedfilter_non_optimizable.steps
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64 max $methods.section_matchedfilter_non_optimizable.max
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65 snthresh $methods.section_matchedfilter_non_optimizable.snthresh
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66 #end if
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67
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68 @COMMAND_LOG_EXIT@
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69 ]]></command>
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70
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71 <inputs>
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72
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73 <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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74
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75 <param name="samplebyclass" type="integer" value="2" label="Number of samples used per class to estimate the best parameters" help="Set to 0 to use the whole dataset. To save time, reduce this number" />
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76
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77 <conditional name="methods">
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78 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
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79 <option value="centWave" >centWave</option>
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80 <option value="matchedFilter" selected="true">matchedFilter</option>
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81 </param>
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82
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83 <!-- centWave Filter options -->
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84 <when value="centWave">
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85 <section name="section_centwave_optiomizable" title="Optimizable parameters" expanded="True">
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86 <conditional name="conditional_parameter">
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87 <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values">
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88 <option value="ppm">Max tolerated ppm m/z deviation in consecutive scans in ppm [ppm]</option>
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89 <option value="peakwidth">Min,Max peak width in seconds [peakwidth]</option>
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90 <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option>
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91 </param>
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92 <when value="ppm">
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93 <param name="ppm" type="text" value="17,32" label="Range for Max tolerated ppm m/z deviation in consecutive scans in ppm" optional="false" help="[ppm] (ex: 25 or 17,32)">
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94 <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator>
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95 </param>
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96 <expand macro="centwave_peakwidth_fixed" />
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97 <expand macro="centwave_mzdiff_fixed" />
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98 </when>
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99 <when value="peakwidth">
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100 <param name="min_peakwidth" type="text" value="12,18" label="Range for Min peak width range in seconds" optional="true" help="[min_peakwidth] (ex: 12,18)">
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101 <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator>
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102 </param>
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103 <param name="max_peakwidth" type="text" value="35,65" label="Range for Max peak width range in seconds" optional="true" help="[max_peakwidth] (ex: 35,65)">
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104 <validator type="regex" message="Should be one combinaison of those format: XX,YY or XX.XX,YY.YY">[0-9]+[\.]?[0-9]*,[0-9]+[\.]?[0-9]*</validator>
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105 </param>
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106 <expand macro="centwave_ppm_fixed" />
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107 <expand macro="centwave_mzdiff_fixed" />
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108 </when>
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109 <when value="mzdiff">
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110 <param name="mzdiff" type="text" value="-0.001,0.010" label="Range for Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap (ex: -0.001,0.010)">
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111 <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator>
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112 </param>
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113 <expand macro="centwave_ppm_fixed" />
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114 <expand macro="centwave_peakwidth_fixed" />
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115 </when>
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116 </conditional>
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117 </section>
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118
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119 <section name="section_centwave_non_optiomizable" title="Non optimizable parameters" expanded="True">
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120 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
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121 <param name="integrate" type="select" label="Peak limits method" help="[integrate]" >
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122 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
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123 <option value="2">peak limits based on real data (more sensitive to noise)</option>
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124 </param>
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125 <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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126 <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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127 </section>
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128 </when>
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129
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130 <!-- matched Filter options -->
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131 <when value="matchedFilter">
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132 <section name="section_matchedfilter_optiomizable" title="Optimizable parameters" expanded="True">
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133 <conditional name="conditional_parameter">
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134 <param name="select_parameter" type="select" label="Which parameter do you want to optimize?" help="Only one paramter can be optimized at once. The other will require fixed values">
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135 <option value="fwhm">Full width at half maximum of matched filtration gaussian model peak [fwhm]</option>
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136 <option value="mzdiff">Minimum difference in m/z for peaks with overlapping Retention Times [mzdiff]</option>
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137 </param>
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138 <when value="fwhm">
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139 <param name="fwhm" type="text" value="25,35" label="Range for Full width at half maximum of matched filtration gaussian model peak" optional="true" help="[fwhm] Only used to calculate the actual sigma (ex: 25,35)">
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140 <validator type="regex" message="Should be this format: XX,YY">[0-9]+,[0-9]+</validator>
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141 </param>
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142 <expand macro="matchedfilter_mzdiff_fixed" />
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143 </when>
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144 <when value="mzdiff">
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145 <param name="mzdiff" type="text" value="0.4,0.7" label="Range for Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps (ex: 0.4,0.7)">
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146 <validator type="regex" message="Should be one combinaison of those format: XX,YY or -XX,YY or XX.XX,YY.YY">[\-]?[0-9]+[\.]?[0-9]*,[\-]?[0-9]+[\.]?[0-9]*</validator>
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147 </param>
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148 <expand macro="matchedfilter_fwhm_fixed" />
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149 </when>
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150 </conditional>
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151 </section>
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152
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153 <section name="section_matchedfilter_non_optimizable" title="Non optimizable parameters" expanded="True">
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154 <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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155 <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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156 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
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157 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
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158 </section>
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159 </when>
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160 </conditional>
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161
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162
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163 </inputs>
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164
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165 <outputs>
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166 <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
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167 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
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168 <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
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169 </outputs>
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170
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171 <tests>
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172 <test>
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173 <param name="input" value="MM14.mzML" ftype="mzxml" />
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174 <param name="samplebyclass" value="0" />
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175 <conditional name="methods">
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176 <param name="method" value="centWave" />
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177 <section name="section_centwave_optiomizable" >
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178 <conditional name="conditional_parameter">
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179 <param name="select_parameter" value="peakwidth" />
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180 <param name="min_peakwidth" value="3,9.5" />
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181 <param name="max_peakwidth" value="10,20" />
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182 <param name="ppm" value="56" />
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183 <param name="mzdiff" value="-0.001" />
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184 </conditional>
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185 </section>
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186 </conditional>
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187 <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_peakwidth.tsv" />
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188 </test>
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189 <test>
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190 <param name="input" value="MM14.mzML" ftype="mzxml" />
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191 <param name="samplebyclass" value="0" />
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192 <conditional name="methods">
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193 <param name="method" value="centWave" />
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194 <section name="section_centwave_optiomizable" >
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195 <conditional name="conditional_parameter">
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196 <param name="select_parameter" value="ppm" />
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197 <param name="ppm" value="50,60" />
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198 <param name="min_peakwidth" value="3.325" />
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199 <param name="max_peakwidth" value="11" />
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200 <param name="mzdiff" value="-0.001" />
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201 </conditional>
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202 </section>
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203 </conditional>
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204 <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet_ppm.tsv" />
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205 </test>
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206 <!-- Too long for Travis CI -->
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207 <!--<test>
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208 <param name="inputs|input" value="zip_file" />
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209 <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" />
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210 <param name="samplebyclass" value="1" />
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211 <param name="methods|method" value="centWave" />
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212 <param name="methods|ppm" value="25" />
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213 <param name="methods|min_peakwidth" value="20,30" />
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214 <param name="methods|max_peakwidth" value="45,55" />
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215 <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" />
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216 </test>-->
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217 <!-- Too long for Travis CI -->
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218 <!--<test>
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219 <param name="inputs|input" value="zip_file" />
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220 <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" />
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221 <param name="samplebyclass" value="1" />
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222 <param name="methods|method" value="matchedFilter" />
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223 <param name="methods|step" value="0.05,0.15" />
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224 <param name="methods|fwhm" value="25,35" />
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225 <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" />
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226 </test>-->
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227 <!--Failed:
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228 Error in resultIncreased(history) :
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229 No isotopes have been detected, peak picking not optimizable by IPO!-->
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230 <!--<test>
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231 <param name="inputs|input" value="zip_file" />
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232 <param name="inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
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233 <param name="methods|method" value="centWave" />
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234 <param name="methods|ppm" value="25" />
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235 <param name="methods|min_peakwidth" value="15,25" />
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236 <param name="methods|min_peakwidth" value="20,30" />
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237 <param name="methods|max_peakwidth" value="45,55" />
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238 <output name="parametersOutput" file="faahKO_IPO_parameters4xcmsSet.tsv" />
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239 </test>-->
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240 </tests>
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241
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242 <help><![CDATA[
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243
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244 @HELP_AUTHORS@
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245
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246 ===============
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247 IPO.ipo4xcmsSet
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248 ===============
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249
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250 -----------
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251 Description
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252 -----------
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253
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254 A Tool for automated Optimization of XCMS Parameters
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255
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256
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257 -----------------
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258 Workflow position
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259 -----------------
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260
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261 **Upstream tools**
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262
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263 ========================= ================= ======= =========
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264 Name output file format parameter
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265 ========================= ================= ======= =========
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266 NA NA zip NA
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267 ========================= ================= ======= =========
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268
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269
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270 **Downstream tools**
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271
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272 +---------------------------+----------------------+-----------------+
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273 | Name | Output file | Format |
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274 +===========================+======================+=================+
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275 |xcms.xcmsSet | parametersOutput.tsv | Tabular |
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276 +---------------------------+--------------------+-------------------+
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277
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278
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279
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280 -----------
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281 Input files
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282 -----------
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283
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284 +---------------------------+------------+
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285 | Parameter : num + label | Format |
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286 +===========================+============+
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287 | 1 : Choose your inputs | zip |
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288 +---------------------------+------------+
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289
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290 **Choose your inputs**
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291
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292 You have two methods for your inputs:
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293
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294 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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295 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
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296
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297 Steps for creating the zip file
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298 -------------------------------
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299
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300 **Step1: Creating your directory and hierarchize the subdirectories**
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301
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302
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303 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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304
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305 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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306 arabidopsis/wild/01.raw
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307 arabidopsis/mutant/01.raw
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308
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309 **Step2: Creating a zip file**
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310
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311 Create your zip file (e.g.: arabidopsis.zip).
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312
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313 **Step 3 : Uploading it to our Galaxy server**
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314
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315 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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316
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317 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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318
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319 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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320
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321 Advices for converting your files for the XCMS input
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322 ----------------------------------------------------
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323
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324 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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325
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326 **We recommend you the following parameters:**
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327
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328 Use Filtering: **True**
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329
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330 Use Peak Picking: **True**
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331
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332 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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333
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334 Use zlib: **64**
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335
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336 Binary Encoding: **64**
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337
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338 m/z Encoding: **64**
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339
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340 Intensity Encoding: **64**
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341
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342
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343 ----------
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344 Parameters
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345 ----------
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346
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347 Extraction method for peaks detection
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348 -------------------------------------
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349
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350 **Matched Filter**
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351
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352 | 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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353 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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354
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355
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356 **cent Wave**
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357
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358 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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359 | Due to the fact that peak centroids are used, a binning step is not necessary.
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360 | 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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361
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362
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363 ------------
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364 Output files
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365 ------------
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366
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367 IPO_parameters4xcmsSet.tsv
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368
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369 | Optimal parameters for xcmsSet
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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 Changelog/News
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375 --------------
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376
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377
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378
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379 ]]></help>
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380
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381 <expand macro="citation" />
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382 </tool>