Mercurial > repos > lecorguille > ipo

annotate ipo4xcmsSet.xml @ 3:9f1e18bc8ce3 draft

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author lecorguille
date Thu, 28 Jul 2016 11:03:04 -0400
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children 9fa5856f6184
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1 <tool id="ipo4xcmsSet" name="IPO for xcmsSet" version="2.0.8">
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2
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3 <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
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11
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12 <command><![CDATA[
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13 @COMMAND_SCRIPT@
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14
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15 #if $inputs.input == "zip_file":
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16 zipfile $inputs.zip_file
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17 #elif $inputs.input == "single_file":
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18 singlefile_galaxyPath $inputs.single_file singlefile_sampleName $inputs.single_file.name
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19 #end if
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20
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21 parametersOutput $parametersOutput
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22
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23 samplebyclass $samplebyclass
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24
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25 ## profmethod $profmethod
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26 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
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27 #if $methods.method == "centWave":
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28 ppm $methods.ppm
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29 min_peakwidth "c($methods.min_peakwidth)"
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30 max_peakwidth "c($methods.max_peakwidth)"
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31 #elif $methods.method == "matchedFilter":
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32 step $methods.step
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33 fwhm $methods.fwhm
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34 #end if
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35
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36 @COMMAND_LOG_EXIT@ 2> /tmp/log.err
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37 ]]></command>
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38
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39 <inputs>
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40
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41 <conditional name="inputs">
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42 <param name="input" type="select" label="Choose your inputs method" >
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43 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
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44 <option value="single_file">mzXML file from your history</option>
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45 </param>
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46 <when value="zip_file">
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47 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
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48 </when>
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49 <when value="single_file">
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50 <param name="single_file" type="data" format="mzxml" label="Single file" />
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51 </when>
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52 </conditional>
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53
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54 <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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55
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56 <conditional name="methods">
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57 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
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58 <option value="centWave" >centWave</option>
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59 <option value="matchedFilter" selected="true">matchedFilter</option>
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60 </param>
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61
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62 <!-- centWave Filter options -->
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63 <when value="centWave">
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64 <param name="ppm" type="text" value="5,25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" optional="false" />
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65 <param name="min_peakwidth" type="text" value="15,25" label="Min peak width range in seconds" help="[peakwidth]" optional="true" />
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66 <param name="max_peakwidth" type="text" value="45,55" label="Max peak width range in seconds" help="[peakwidth]" optional="true" />
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67 </when>
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68
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69 <!-- matched Filter options -->
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70 <when value="matchedFilter">
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71 <param name="step" type="float" value="0.01" 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" optional="true" />
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72 <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" optional="true" />
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73 </when>
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74 </conditional>
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75
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76
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77 </inputs>
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78
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79 <outputs>
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80 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
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81 <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
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82 </outputs>
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83
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84 <tests>
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85 <test>
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86 <param name="inputs|input" value="single_file" />
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87 <param name="inputs|single_file" value="MM14.mzML" ftype="mzxml" />
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88 <param name="methods|method" value="centWave" />
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89 <param name="methods|ppm" value="56" />
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90 <param name="methods|min_peakwidth" value="3,9.5" />
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91 <param name="methods|max_peakwidth" value="10,20" />
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92 <output name="parametersOutput" file="MM14_IPO_parameters4xcmsSet.tsv" />
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93 </test>
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94 <!--Failed:
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95 Error in resultIncreased(history) :
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96 No isotopes have been detected, peak picking not optimizable by IPO!-->
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97 <!--<test>
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98 <param name="inputs|input" value="zip_file" />
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99 <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" />
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100 <param name="samplebyclass" value="1" />
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101 <param name="methods|method" value="centWave" />
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102 <param name="methods|ppm" value="25" />
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103 <param name="methods|min_peakwidth" value="20,30" />
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104 <param name="methods|max_peakwidth" value="45,55" />
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105 <output name="parametersOutput" file="sacuri_2files_centWave_IPO_parameters4xcmsSet.tsv" />
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106 </test>-->
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107 <!-- Too long for Travis CI -->
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108 <!--<test>
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109 <param name="inputs|input" value="zip_file" />
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110 <param name="inputs|zip_file" value="sacuri_2files.zip" ftype="zip" />
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111 <param name="samplebyclass" value="1" />
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112 <param name="methods|method" value="matchedFilter" />
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113 <param name="methods|step" value="0.01" />
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114 <param name="methods|fwhm" value="4" />
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115 <output name="parametersOutput" file="sacuri_2files_matchedFilter_IPO_parameters4xcmsSet.tsv" />
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116 </test>-->
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117 </tests>
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118
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119 <help><![CDATA[
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120
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121 @HELP_AUTHORS@
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122
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123 ===============
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124 IPO.ipo4xcmsSet
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125 ===============
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126
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127 -----------
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128 Description
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129 -----------
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130
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131 A Tool for automated Optimization of XCMS Parameters
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132
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133
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134 -----------------
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135 Workflow position
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136 -----------------
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137
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138 **Upstream tools**
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139
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140 ========================= ================= ======= =========
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141 Name output file format parameter
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142 ========================= ================= ======= =========
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143 NA NA zip NA
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144 ========================= ================= ======= =========
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145
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146
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147 **Downstream tools**
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148
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149 +---------------------------+----------------------+-----------------+
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150 | Name | Output file | Format |
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151 +===========================+======================+=================+
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152 |xcms.xcmsSet | parametersOutput.tsv | Tabular |
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153 +---------------------------+--------------------+-------------------+
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154
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155
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156
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157 -----------
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158 Input files
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159 -----------
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160
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161 +---------------------------+------------+
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162 | Parameter : num + label | Format |
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163 +===========================+============+
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164 | 1 : Choose your inputs | zip |
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165 +---------------------------+------------+
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166
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167 **Choose your inputs**
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168
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169 You have two methods for your inputs:
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170
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171 | 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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172 | 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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173
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174 Steps for creating the zip file
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175 -------------------------------
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176
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177 **Step1: Creating your directory and hierarchize the subdirectories**
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178
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179
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180 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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181
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182 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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183 arabidopsis/wild/01.raw
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184 arabidopsis/mutant/01.raw
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185
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186 **Step2: Creating a zip file**
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187
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188 Create your zip file (e.g.: arabidopsis.zip).
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189
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190 **Step 3 : Uploading it to our Galaxy server**
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191
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192 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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193
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194 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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195
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196 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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197
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198 Advices for converting your files for the XCMS input
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199 ----------------------------------------------------
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200
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201 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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202
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203 **We recommend you the following parameters:**
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204
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205 Use Filtering: **True**
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206
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207 Use Peak Picking: **True**
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208
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209 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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210
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211 Use zlib: **64**
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212
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213 Binary Encoding: **64**
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214
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215 m/z Encoding: **64**
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216
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217 Intensity Encoding: **64**
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218
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219
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220 ----------
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221 Parameters
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222 ----------
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223
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224 Extraction method for peaks detection
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225 -------------------------------------
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226
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227 **Matched Filter**
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228
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229 | 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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230 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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231
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232
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233 **cent Wave**
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234
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235 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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236 | Due to the fact that peak centroids are used, a binning step is not necessary.
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237 | 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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240 ------------
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241 Output files
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242 ------------
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243
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244 IPO_parameters4xcmsSet.tsv
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245
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246 | Optimal parameters for xcmsSet
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247
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248
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249 ---------------------------------------------------
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250
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251 Changelog/News
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252 --------------
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255
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256 ]]></help>
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257
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258 <expand macro="citation" />
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259 </tool>