Mercurial > repos > lecorguille > ipo

annotate ipo4retgroup.xml @ 6:03fdfbd914ab draft

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author lecorguille
date Thu, 30 Mar 2017 11:27:09 -0400
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children dd0a593dded1
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1 <tool id="ipo4retgroup" name="IPO for group and retcor" version="0.0.1">
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2
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3 <description>IPO optimization process for xcms.group and xcms.retcor</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 LANG=C Rscript $__tool_directory__/ipo4retgroup.r
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14
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15 image '$image'
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16
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17 parametersOutput '$parametersOutput'
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18
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19 samplebyclass $samplebyclass
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20
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21 @COMMAND_NSLAVES@
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22
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23 ## group methods
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24
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25 sleep 0.001
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26 #if $group.methods.method == "density":
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27 bw "c($group.methods.bw)"
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28 minfrac "c($group.methods.minfrac)"
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29 mzwid "c($group.methods.mzwid)"
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30 ## minsamp "c($group.methods.minsamp)"
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31 #if $group.methods.density_options.option == "show":
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32 max "c($group.methods.density_options.max)"
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33 #end if
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34 #end if
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36
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37
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38 ## retcor methods
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39
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40 #if $retcor.methods.method == "obiwarp":
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41 retcorMethod obiwarp
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42 profStep "c($methods.profStep)"
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43
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44 ## $distFunc [1] "cor_opt"
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45 ## $gapInit [1] 0.0 0.4
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46 ## $gapExtend [1] 2.1 2.7
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47 ## $$plottype [1] "none"
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48 ## $response [1] 1
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49 ## $factorDiag [1] 2
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50 ## $factorGap [1] 1
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51 ## $localAlignment [1] 0
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52
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53 #elif $retcor.methods.method == "peakgroups":
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54 ## smooth loess
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55 retcorMethod loess
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56 smooth loess
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57 extra "c($retcor.methods.extra)"
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58 missing "c($retcor.methods.missing)"
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59 #if $retcor.methods.options.option == "show":
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60 span "c($retcor.methods.options.span)"
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61 family "$retcor.methods.options.family"
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62 plottype "$retcor.methods.options.plottype"
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63 #end if
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64 #elif $retcor.methods.method == "none":
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65 retcorMethod none
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66 #end if
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67
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68 @COMMAND_FILE_LOAD@
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69
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70 @COMMAND_LOG_EXIT@
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71 ]]></command>
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72
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73 <inputs>
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74
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75 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
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76
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77 <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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78
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79 <section name="group" title="Group Options" expanded="False">
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80
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81 <conditional name="methods">
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82 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below">
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83 <option value="density" selected="true">density</option>
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84 </param>
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85 <when value="density">
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86 <param name="bw" type="text" value="22,38" label="Range for Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram (ex: 30 or 22,38)" />
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87 <param name="minfrac" type="text" value="0.3,0.7" label="Range for Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group (ex: 0.5 or 0.3,0.7)" />
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88 <param name="mzwid" type="text" value="0.015,0.035" label="Range for Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples (ex: 0.25 or 0.015,0.035)" />
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89 <!--
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90 <param name="minsamp" type="hidden" value="1" label="Range for Minimum number of samples necessary in at least one of the sample groups for it to be a valid group" help="[minsamp] (ex: 1 or 0,5" />
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91 -->
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92 <conditional name="density_options">
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93 <param name="option" type="select" label="Advanced options">
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94 <option value="show">show</option>
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95 <option value="hide" selected="true">hide</option>
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96 </param>
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97 <when value="show">
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98 <param name="max" type="text" value="50" label="Range for Maximum number of groups to identify in a single m/z slice" help="[max] (ex: 50 or 25,75)" />
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99 </when>
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100 <when value="hide">
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101 </when>
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102 </conditional>
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103
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104 </when>
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105 </conditional>
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106
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107
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108 </section>
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109
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110 <section name="retcor" title="Retcor Options" expanded="False">
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111 <conditional name="methods">
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112 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
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113 <option value="obiwarp">obiwarp</option>
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114 <option value="peakgroups">peakgroups</option>
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115 </param>
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116 <when value="obiwarp">
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117 <param name="profStep" type="text" value="0.7,1.0" label="Range for Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files (ex: 1 or 0.7 1.0)" />
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118 <!--
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119 ## $distFunc [1] "cor_opt"
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120 ## $gapInit [1] 0.0 0.4
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121 ## $gapExtend [1] 2.1 2.7
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122 ## $$plottype [1] "none"
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123 ## $response [1] 1
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124 ## $factorDiag [1] 2
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125 ## $factorGap [1] 1
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126 ## $localAlignment [1] 0
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127 -->
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128 </when>
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129 <when value="peakgroups">
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130 <param name="smooth" type="select" label="Smooth method" help="[smooth] either 'loess’ for non-linear alignment or ‘linear’ for linear alignment" >
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131 <option value="loess">loess</option>
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132 </param>
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133 <param name="extra" type="text" value="1" label="Range for Number of extra peaks to allow in retention time correction correction groups" help="[extra] (ex: 1 or 1,3)" />
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134 <param name="missing" type="text" value="1" label="Range for Number of missing samples to allow in retention time correction groups" help="[missing] (ex: 1or 1,3)" />
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135
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136 <conditional name="options">
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137 <param name="option" type="select" label="Advanced options">
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138 <option value="show">show</option>
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139 <option value="hide" selected="true">hide</option>
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140 </param>
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141 <when value="show">
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142 <param name="span" type="text" value="0.1,0.3" label="Range for Degree of smoothing for local polynomial regression fitting" help="[span] (ex: 0.2 or 0.1,0.3)"/>
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143 <!-- @TODO multiple="true" -->
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144 <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
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145 <option value="gaussian" selected="true">gaussian</option>
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146 <option value="symmetric">symmetric</option>
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147 </param>
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148 <!-- @TODO multiple="true" -->
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149 <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
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150 <option value="none" selected="true">none</option>
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151 <option value="deviation">deviation</option>
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152 <option value="mdevden">mdevden</option>
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153 </param>
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154
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155 </when>
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156 <when value="hide">
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157 </when>
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158 </conditional>
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159 </when>
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160 </conditional>
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161
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162 </section>
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163
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164 <expand macro="file_load"/>
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165
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166 </inputs>
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167
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168 <outputs>
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169 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
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170 <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
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171 </outputs>
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172
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173 <tests>
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174 <!-- TOO LONG
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175 <test>
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176 <param name="image" value="faahKO.xset.RData"/>
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177 <param name="group|methods|method" value="density"/>
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178 <param name="group|methods|bw" value="28,32"/>
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179 <param name="group|methods|minfrac" value="1"/>
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180 <param name="group|methods|mzwid" value="0.15,0.35"/>
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181 <param name="retcor|methods|method" value="peakgroups"/>
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182 <param name="retcor|methods|smooth" value="loess"/>
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183 <param name="retcor|methods|extra" value="1"/>
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184 <param name="retcor|methods|missing" value="1"/>
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185 <param name="file_load_conditional|file_load_select" value="yes" />
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186 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
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187 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" />
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188 </test>-->
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189
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190 <test>
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191 <param name="image" value="faahKO.xset.RData"/>
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192 <param name="group|methods|method" value="density"/>
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193 <param name="group|methods|bw" value="28,32"/>
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194 <param name="group|methods|minfrac" value="1"/>
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195 <param name="group|methods|mzwid" value="0.25"/>
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196 <param name="retcor|methods|method" value="peakgroups"/>
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197 <param name="retcor|methods|smooth" value="loess"/>
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198 <param name="retcor|methods|extra" value="1"/>
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199 <param name="retcor|methods|missing" value="1"/>
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200 <param name="file_load_conditional|file_load_select" value="yes" />
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201 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
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202 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" />
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203 </test>
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204
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205 <test>
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206 <param name="image" value="faahKO.xset.RData"/>
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207 <param name="group|methods|method" value="density"/>
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208 <param name="group|methods|bw" value="30"/>
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209 <param name="group|methods|minfrac" value="1"/>
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210 <param name="group|methods|mzwid" value="0.15,0.35"/>
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211 <param name="retcor|methods|method" value="peakgroups"/>
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212 <param name="retcor|methods|smooth" value="loess"/>
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213 <param name="retcor|methods|extra" value="1"/>
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214 <param name="retcor|methods|missing" value="1"/>
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215 <param name="file_load_conditional|file_load_select" value="yes" />
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216 <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" />
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217 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" />
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218 </test>
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219
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220 <!--<test>
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221 <param name="image" value="MM-xset-merge.RData"/>
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222 <param name="group|methods|method" value="density"/>
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223 <param name="group|methods|bw" value="22,38"/>
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224 <param name="group|methods|minfrac" value="1"/>
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225 <param name="group|methods|mzwid" value="0.015,0.035"/>
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226 <param name="retcor|methods|method" value="peakgroups"/>
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227 <param name="retcor|methods|smooth" value="loess"/>
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228 <param name="retcor|methods|extra" value="1"/>
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229 <param name="retcor|methods|missing" value="1"/>
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230 <param name="file_load_conditional|file_load_select" value="yes" />
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231 <param name="file_load_conditional|inputs|input" value="single_file" />
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232 <param name="file_load_conditional|inputs|single_file" value="MM8.mzML,MM14.mzML" ftype="mzxml" />
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233 <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" />
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234 </test>-->
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235 </tests>
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236
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237 <help><![CDATA[
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238
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239 @HELP_AUTHORS@
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240
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241 ===============
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242 IPO.ipo4xcmsSet
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243 ===============
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244
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245 -----------
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246 Description
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247 -----------
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248
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249 A Tool for automated Optimization of XCMS Parameters
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250
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251
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252 -----------------
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253 Workflow position
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254 -----------------
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255
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256 **Upstream tools**
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257
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258 ========================= ================= ======= =========
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259 Name output file format parameter
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260 ========================= ================= ======= =========
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261 NA NA zip NA
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262 ========================= ================= ======= =========
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263
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264
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265 **Downstream tools**
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266
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267 +---------------------------+----------------------+-----------------+
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268 | Name | Output file | Format |
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269 +===========================+======================+=================+
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270 |xcms.xcmsSet | parametersOutput.tsv | Tabular |
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271 +---------------------------+--------------------+-------------------+
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272
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273
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274
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275 -----------
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276 Input files
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277 -----------
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278
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279 +---------------------------+------------+
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280 | Parameter : num + label | Format |
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281 +===========================+============+
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282 | 1 : Choose your inputs | zip |
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283 +---------------------------+------------+
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284
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285 **Choose your inputs**
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286
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287 You have two methods for your inputs:
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288
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289 | 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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290 | 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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291
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292 Steps for creating the zip file
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293 -------------------------------
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294
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295 **Step1: Creating your directory and hierarchize the subdirectories**
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296
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297
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298 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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299
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300 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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301 arabidopsis/wild/01.raw
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302 arabidopsis/mutant/01.raw
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303
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304 **Step2: Creating a zip file**
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305
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306 Create your zip file (e.g.: arabidopsis.zip).
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307
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308 **Step 3 : Uploading it to our Galaxy server**
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309
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310 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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311
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312 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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313
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314 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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315
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316 Advices for converting your files for the XCMS input
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317 ----------------------------------------------------
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318
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319 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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320
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321 **We recommend you the following parameters:**
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322
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323 Use Filtering: **True**
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324
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325 Use Peak Picking: **True**
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326
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327 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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328
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329 Use zlib: **64**
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330
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331 Binary Encoding: **64**
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332
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333 m/z Encoding: **64**
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334
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335 Intensity Encoding: **64**
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336
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337
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338 ----------
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339 Parameters
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340 ----------
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341
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342 Extraction method for peaks detection
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343 -------------------------------------
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344
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345 **Matched Filter**
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346
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347 | 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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348 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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349
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350
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351 **cent Wave**
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352
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353 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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354 | Due to the fact that peak centroids are used, a binning step is not necessary.
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355 | 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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356
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357
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358 ------------
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359 Output files
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360 ------------
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361
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362 IPO_parameters4xcmsSet.tsv
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363
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364 | Optimal parameters for xcmsSet
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365
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366
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367 ---------------------------------------------------
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368
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369 Changelog/News
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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 ]]></help>
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375
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
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376 <expand macro="citation" />
03fdfbd914ab planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
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377 </tool>