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annotate ipo4retgroup.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="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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8 <macro name="group_density_bw_fixed">
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9 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" />
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10 </macro>
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11
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12 <macro name="group_density_mzwid_fixed">
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13 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " />
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14 </macro>
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15 </macros>
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16
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17 <expand macro="requirements"/>
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18 <expand macro="stdio"/>
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19
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20 <command><![CDATA[
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21 LANG=C Rscript $__tool_directory__/ipo4retgroup.r
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22
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23 image '$image'
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24
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25 parametersOutput '$parametersOutput'
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26
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27 samplebyclass $samplebyclass
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28
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29 @COMMAND_NSLAVES@
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30
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31 ## group methods
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32
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33 sleep 0.001
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34 #if $group.methods.method == "density":
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35 bw "c($group.methods.section_group_density_optiomizable.conditional_parameter.bw)"
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36 mzwid "c($group.methods.section_group_density_optiomizable.conditional_parameter.mzwid)"
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37
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38 minfrac $group.methods.section_group_density_non_optimizable.minfrac
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39 max $group.methods.section_group_density_non_optimizable.max
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40 #end if
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41
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42 ## retcor methods
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43
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44 #if $retcor.methods.method == "obiwarp":
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45 retcorMethod obiwarp
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46 profStep $methods.section_retcor_obiwarp_non_optimizable.profStep
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47
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48 #elif $retcor.methods.method == "peakgroups":
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49 retcorMethod loess
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50 smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth
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51 extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra
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52 missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing
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53 span $retcor.methods.section_retcor_peakgroups_non_optimizable.span
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54 family $retcor.methods.section_retcor_peakgroups_non_optimizable.family
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55 plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype
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56 #elif $retcor.methods.method == "none":
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57 retcorMethod none
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58 #end if
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59
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60 @COMMAND_FILE_LOAD@
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61
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62 @COMMAND_LOG_EXIT@
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63 ]]></command>
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64
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65 <inputs>
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66
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67 <param name="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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68
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69 <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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70
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71 <section name="group" title="Group Options" expanded="True">
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72 <conditional name="methods">
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73 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below. Only the density method is available so far">
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74 <option value="density" selected="true">density</option>
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75 </param>
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76 <when value="density">
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77 <section name="section_group_density_optiomizable" title="Optimizable parameters" expanded="True">
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78 <conditional name="conditional_parameter">
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79 <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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80 <option value="bw">Bandwidth [bw]</option>
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81 <option value="mzwid">Width of overlapping m/z slices [mzwid]</option>
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82 </param>
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83 <when value="bw">
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84 <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: 22,38)">
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85 <validator type="regex" message="Should be this format XX,YY">[0-9]+,[0-9]+</validator>
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86 </param>
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87 <expand macro="group_density_mzwid_fixed" />
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88 </when>
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89 <when value="mzwid">
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90 <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: 0.015,0.035)" >
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91 <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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92 </param>
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93 <expand macro="group_density_bw_fixed" />
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94 </when>
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95 </conditional>
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96 </section>
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97 <section name="section_group_density_non_optimizable" title="Non optimizable parameters" expanded="True">
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98 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" />
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99 <param name="max" type="integer" value="50" label="Maximum number of groups to identify in a single m/z slice" help="[max]" />
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100 </section>
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101 </when>
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102 </conditional>
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103 </section>
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104
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105 <section name="retcor" title="Retcor Options" expanded="True">
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106 <conditional name="methods">
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107 <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
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108 <option value="obiwarp">obiwarp</option>
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109 <option value="peakgroups">peakgroups</option>
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110 </param>
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111 <when value="obiwarp">
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112 <section name="section_retcor_obiwarp_non_optimizable" title="Non optimizable parameters" expanded="True">
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113 <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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114 </section>
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115 </when>
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116 <when value="peakgroups">
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117 <section name="section_retcor_peakgroups_non_optimizable" title="Non optimizable parameters" expanded="True">
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118 <param name="smooth" type="select" label="Smooth method" help="[smooth] only the 'loess’ for non-linear alignment is available so far" >
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119 <option value="loess">loess</option>
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120 </param>
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121 <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" />
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122 <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" />
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123 <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
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124 <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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125 <option value="gaussian" selected="true">gaussian</option>
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126 <option value="symmetric">symmetric</option>
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127 </param>
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128 <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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129 <option value="none" selected="true">none</option>
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130 <option value="deviation">deviation</option>
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131 <option value="mdevden">mdevden</option>
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132 </param>
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133 </section>
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134 </when>
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135 </conditional>
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136
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137 </section>
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138
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139 <expand macro="input_file_load"/>
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140
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141 </inputs>
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142
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143 <outputs>
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144 <data name="parametersOutput" format="tabular" label="IPO_parameters4xcmsSet.tsv" />
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145 <data name="log" format="txt" label="ipo4xcmsSet.log.txt" />
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146 </outputs>
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147
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148 <tests>
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149 <!-- TOO LONG
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150 <test>
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151 <param name="image" value="faahKO.xset.RData"/>
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152 <param name="group|methods|method" value="density"/>
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153 <param name="group|methods|bw" value="28,32"/>
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154 <param name="group|methods|minfrac" value="1"/>
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155 <param name="group|methods|mzwid" value="0.15,0.35"/>
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156 <param name="retcor|methods|method" value="peakgroups"/>
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157 <param name="retcor|methods|smooth" value="loess"/>
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158 <param name="retcor|methods|extra" value="1"/>
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159 <param name="retcor|methods|missing" value="1"/>
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160 <expand macro="test_file_load_zip"/>
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161 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup.tsv" />
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162 </test>-->
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163
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164 <test>
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165 <param name="image" value="faahKO.xset.RData"/>
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166 <section name="group">
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167 <conditional name="methods">
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168 <param name="method" value="density"/>
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169 <section name="section_group_density_optiomizable">
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170 <conditional name="conditional_parameter">
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171 <param name="bw" value="28,32"/>
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172 <param name="mzwid" value="0.25"/>
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173 </conditional>
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174 </section>
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175 <section name="section_group_density_non_optimizable">
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176 <param name="minfrac" value="1"/>
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177 </section>
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178 </conditional>
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179 </section>
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180 <section name="retcor">
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181 <conditional name="methods">
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182 <param name="method" value="peakgroups"/>
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183 <section name="section_retcor_peakgroups_non_optimizable">
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184 <param name="smooth" value="loess"/>
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185 <param name="rextra" value="1"/>
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186 <param name="missing" value="1"/>
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187 </section>
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188 </conditional>
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189 </section>
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190 <expand macro="test_file_load_zip"/>
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191 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_bw.tsv" />
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192 </test>
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193
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194 <!--<test>
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195 <param name="image" value="faahKO.xset.RData"/>
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196 <param name="group|methods|method" value="density"/>
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197 <param name="group|methods|bw" value="30"/>
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198 <param name="group|methods|minfrac" value="1"/>
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199 <param name="group|methods|mzwid" value="0.15,0.35"/>
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200 <param name="retcor|methods|method" value="peakgroups"/>
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201 <param name="retcor|methods|smooth" value="loess"/>
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202 <param name="retcor|methods|extra" value="1"/>
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203 <param name="retcor|methods|missing" value="1"/>
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204 <expand macro="test_file_load_zip"/>
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205 <output name="parametersOutput" file="faahKO_IPO_parameters4retgroup_mzmid.tsv" />
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206 </test>-->
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207
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208 <!--<test>
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209 <param name="image" value="MM-xset-merge.RData"/>
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210 <param name="group|methods|method" value="density"/>
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211 <param name="group|methods|bw" value="22,38"/>
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212 <param name="group|methods|minfrac" value="1"/>
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213 <param name="group|methods|mzwid" value="0.015,0.035"/>
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214 <param name="retcor|methods|method" value="peakgroups"/>
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215 <param name="retcor|methods|smooth" value="loess"/>
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216 <param name="retcor|methods|extra" value="1"/>
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217 <param name="retcor|methods|missing" value="1"/>
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218 <param name="file_load_conditional|file_load_select" value="yes" />
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219 <expand macro="test_file_load_single"/>
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220 <output name="parametersOutput" file="MM_IPO_parameters4retgroup.tsv" />
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221 </test>-->
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222 </tests>
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223
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224 <help><![CDATA[
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225
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226 @HELP_AUTHORS@
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227
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228 ===============
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229 IPO.ipo4xcmsSet
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230 ===============
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231
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232 -----------
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233 Description
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234 -----------
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235
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236 A Tool for automated Optimization of XCMS Parameters
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237
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238
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239 -----------------
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240 Workflow position
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241 -----------------
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242
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243 **Upstream tools**
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244
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245 ========================= ================= ======= =========
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246 Name output file format parameter
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247 ========================= ================= ======= =========
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248 NA NA zip NA
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249 ========================= ================= ======= =========
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250
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251
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252 **Downstream tools**
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253
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254 +---------------------------+----------------------+-----------------+
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255 | Name | Output file | Format |
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256 +===========================+======================+=================+
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257 |xcms.xcmsSet | parametersOutput.tsv | Tabular |
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258 +---------------------------+--------------------+-------------------+
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259
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260
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261
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262 -----------
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263 Input files
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264 -----------
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265
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266 +---------------------------+------------+
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267 | Parameter : num + label | Format |
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268 +===========================+============+
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269 | 1 : Choose your inputs | zip |
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270 +---------------------------+------------+
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271
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272 **Choose your inputs**
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273
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274 You have two methods for your inputs:
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275
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276 | 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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277 | 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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278
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279 Steps for creating the zip file
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280 -------------------------------
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281
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282 **Step1: Creating your directory and hierarchize the subdirectories**
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283
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284
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285 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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286
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287 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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288 arabidopsis/wild/01.raw
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289 arabidopsis/mutant/01.raw
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290
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291 **Step2: Creating a zip file**
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292
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293 Create your zip file (e.g.: arabidopsis.zip).
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294
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295 **Step 3 : Uploading it to our Galaxy server**
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296
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297 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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298
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299 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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300
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301 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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302
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303 Advices for converting your files for the XCMS input
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304 ----------------------------------------------------
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305
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306 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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307
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308 **We recommend you the following parameters:**
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309
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310 Use Filtering: **True**
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311
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312 Use Peak Picking: **True**
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313
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314 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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315
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316 Use zlib: **64**
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317
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318 Binary Encoding: **64**
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319
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320 m/z Encoding: **64**
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321
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322 Intensity Encoding: **64**
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323
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324
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325 ----------
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326 Parameters
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327 ----------
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328
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329 Extraction method for peaks detection
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330 -------------------------------------
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331
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332 **Matched Filter**
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333
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334 | 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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335 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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336
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337
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338 **cent Wave**
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339
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340 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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341 | Due to the fact that peak centroids are used, a binning step is not necessary.
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342 | 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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343
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344
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345 ------------
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346 Output files
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347 ------------
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348
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349 IPO_parameters4xcmsSet.tsv
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350
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351 | Optimal parameters for xcmsSet
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352
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353
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354 ---------------------------------------------------
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355
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356 Changelog/News
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357 --------------
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358
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359
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360
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361 ]]></help>
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362
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363 <expand macro="citation" />
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364 </tool>