Mercurial > repos > tomnl > flag_remove_peaks

annotate flag-remove-peaks.xml @ 10:0302d7e2ce01 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit af689d3f20c86f69aa824545e668280bcd5e0cca-dirty
author tomnl
date Tue, 12 Jun 2018 11:46:01 -0400
parents 2cba35789adf
children e00a33906b3e
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10
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1 <tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.6">
2
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2 <requirements>
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3 <requirement type="package" >r</requirement>
10
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4 <requirement type="package" >r-optparse</requirement>
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5 <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement>
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6 <requirement type="package" version="0.2.5" >r-xcmswrapper</requirement>
2
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7 </requirements>
0
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8 <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
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9 (e.g. RSD of intensity and retention time).
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10 </description>
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11
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12 <stdio>
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13 <exit_code range="1:" />
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14 </stdio>
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15 <command interpreter="Rscript"><![CDATA[
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16 flag-remove-peaks.R
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17 --xset_path=$xset_path
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18
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19 #if $sample_flag.sample_flag=='update'
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20 --rsd_i_sample=$sample_flag.rsd_i_sample
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21 --minfrac_sample=$sample_flag.minfrac_sample
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22 --ithres_sample=$sample_flag.ithres_sample
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23 #end if
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24
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25 #if $blank_flag.blank_flag=='update'
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26 --rsd_i_blank=$blank_flag.rsd_i_blank
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27 --minfrac_blank=$blank_flag.minfrac_blank
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28 --ithres_blank=$blank_flag.ithres_blank
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29 --blank_class=$blank_flag.blank_class
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30 #end if
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31
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32 #if $peak_removal.peak_removal=='remove'
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33 --remove_spectra
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34 --minfrac_xcms=$peak_removal.minfrac_xcms
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35 --mzwid=$peak_removal.mzwid
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36 --bw=$peak_removal.bw
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37 #end if
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38
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39 #if $advanced.advanced=='update'
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40 --egauss_thr=$advanced.egauss_thr
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41 --polarity=$advanced.polarity
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42 --grp_rm_ids=$advanced.grp_rm_ids
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43 --xset_name=$advanced.xset_name
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44 $advanced.temp_save.value
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45
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46 #end if
8
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47 #if $choose_samp.choose_samp=='yes'
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48 --samplelist=$choose_samp.samplelist
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49 #end if
0
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50 ]]></command>
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51 <inputs>
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52 <param type="data" name="xset_path"
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53 help="The path to the xcmsSet object saved as an RData file"/>
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54 <conditional name="sample_flag">
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55 <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
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56 <option value="update" >Update biological sample flag parameters</option>
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57 <option value="" selected="true">Use default biological sample flag parameters</option>
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58 </param>
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59 <when value="">
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60 </when>
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61 <when value="update">
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62 <param name="rsd_i_sample" type="text" label="rsd_i_sample" value="NA"
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63 help="Relative Standard Deviation threshold for the sample classes (--rsd_i_sample)"/>
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64 <param name="minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1"
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65 help="minimum fraction of files for features needed for the sample classes (--minfrac_sample)"/>
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66 <param name="rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA"
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67 help="Relative standard Deviation threshold for the retention time of the sample
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68 classes (--rsd_rt_sample)"/>
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69 <param name="ithres_sample" type="text" label="ithres_sample" value="NA"
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70 help="Intensity threshold for the sample (--ithres_sample)"/>
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71 </when>
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72 </conditional>
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73 <conditional name="blank_flag">
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74 <param name="blank_flag" type="select" label="Change blank flag parameters?">
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75 <option value="update" >Update blank flag parameters</option>
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76 <option value="" selected="true">Use default blank flag parameters</option>
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77 </param>
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78 <when value="">
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79 </when>
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80 <when value="update">
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81 <param name="blank_class" type="text" label="blank_class" value="blank"
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82 help="A string representing the class that will be used for the blank (--blank_class)"/>
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83 <param name="rsd_i_blank" type="text" label="rsd_i_blank" value="NA"
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84 help="RSD threshold for the blank (--rsd_i_blank)"/>
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85 <param name="minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1"
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86 help="minimum fraction of files for features needed for the blank (--minfrac_blank)"/>
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87 <param name="rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA"
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88 help="RSD threshold for the retention time of the blank (--rsd_rt_blank)"/>
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89 <param name="ithres_blank" type="text" label="ithres_blank" value="NA"
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90 help="Intensity threshold for the blank (--ithres_blank)"/>
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91 <param name="s2b" type="float" label="s2b" value="10"
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92 help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
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93 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
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94 1000/10 = 100, so sample has fold change higher than the threshold and the peak
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95 is not considered a blank (--s2b)"/>
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96 </when>
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97 </conditional>
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98 <conditional name="peak_removal">
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99 <param name="peak_removal" type="select" label="Remove peaks from xcmsSet object?">
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100 <option value="remove" >Remove peaks and re-group</option>
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101 <option value="" selected="true">Only flag peaks (do not remove and re-group)</option>
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102 </param>
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103 <when value="">
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104 </when>
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105 <when value="remove">
9
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106 <param name="minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1"
0
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107 help="minfrac for xcms grouping (--minfrac_xcms)"/>
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108 <param name="mzwid" type="float" label="mzwid" value="0.001"
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109 help="mzwid for xcms grouping (--minfrac_xcms)"/>
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110 <param name="bw" type="float" label="bw" value="5"
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111 help="bw for xcms grouping(--minfrac_xcms)"/>
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112 </when>
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113 </conditional>
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114 <conditional name="advanced">
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115 <param name="advanced" type="select" label="Advanced parameters">
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116 <option value="update" >Update advanced and testing parameters</option>
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117 <option value="" selected="true">Use default advanced parameters</option>
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118 </param>
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119 <when value="">
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120 </when>
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121 <when value="update">
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122 <param name="egauss_thr" type="text" label="egauss_thr" value="NA"
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123 help="Threshold for filtering out non gaussian shaped peaks. Note this only works
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124 if the 'verbose columns' and 'fit gauss' was used with xcms (--egauss_thr)"/>
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125 <param name="temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue=""
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126 help="Assign True if files for each step saved (for testing purposes) (--temp_save)"/>
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127 <param name="polarity" type="select" label="polarity"
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128 help="polarity (just used for naming purpose when files are saved) (--polarity)">
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129 <option value="positive">Positive</option>
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130 <option value="negative" >Negative</option>
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131 <option value="NA" selected="true">NA</option>
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132 </param>
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133 <param name="grp_rm_ids" type="text" label="grp_rm_ids" value="NA"
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134 help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output)
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135 e.g '1,20,30,56'
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136 (--grp_rm_ids)"/>
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137 <param name="xset_name" type="text" label="xset_name" value="xset"
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138 help="Name of the xcmsSet object within the RData file (--xset_name)"/>
8
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139 </when>
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140 </conditional>
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141 <conditional name="choose_samp">
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142 <param name="choose_samp" type="select" label="Samplelist">
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143 <option value="yes" >Use samplelist</option>
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144 <option value="" selected="true">Don't use samplelist</option>
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145 </param>
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146 <when value="">
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147 </when>
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148 <when value="yes">
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149 <param name="samplelist" type="data" label="samplelist" format="tsv,tabular"
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150 help="A samplelist can be provided to find an appriopiate blank class (requires a column 'blank' where 'yes' indicates
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151 the class should be used as the blank (--samplelist)"/>
0
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152
8
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153 </when>
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154 </conditional>
0
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155 </inputs>
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156 <outputs>
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157 <data name="peaklist_filtered" format="tabular" label="peaklist_filtered"
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158 from_work_dir="peaklist_filtered.txt" visible="true"/>
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159 <data name="removed_peaks" format="tabular" label="removed_peaks"
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160 from_work_dir="removed_peaks.txt" visible="true"/>
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161 <data name="xset_filtered" format="rdata" label="xset_filtered"
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162 from_work_dir="xset_filtered.RData" visible="true"/>
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163 </outputs>
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164 <tests>
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165 <test>
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166 <param name="blank_flag.blank_flag" value="update" />
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167 <conditional name="blank_flag">
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168 <param name="blank_flag" value="update"/>
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169 <param name="blank_class" value="KO" />
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170 </conditional>
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171 <conditional name="peak_removal">
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172 <param name="peak_removal" value="remove"/>
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173 </conditional>
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174 <param name="xset_path" value="xset.RData" type="rdata" />
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175 <output name="peaklist_filtered" type="tabular" file="peaklist_filtered.tabular">
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176 </output>
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177 <output name="removed_peaks" type="tabular" file="removed_peaks.tabular">
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178 </output>
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179
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180
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181 </test>
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182 </tests>
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183 <help><![CDATA[
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184
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185 =======================================
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186 Flag & remove peaks from xcmsSet object
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187 =======================================
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188 -----------
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189 Description
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190 -----------
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191
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192 Tool to flag XCMS grouped peaks based on various criteria (e.g RSD, intensity). The flagged grouped peaks can then be removed
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193 completely from the xcmsSet object (xset). This means removing the individual peaks associated for each file. Located
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194 in the **xset@peaks** socket of the xcmsSet object.
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195
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196 Additionally a list of ids of the xcms grouped peaks can be supplied, all peaks associated with these ids can be
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197 be removed.
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198
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199 **Note**: grouped peak refers to a peak that has been grouped together by xcms::group function
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200
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201 -----------------
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202 Updated peaklist
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203 -----------------
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204 The calculated columns for the update peaklist dataframe include:
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205
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206 * RSD of intensity for grouped peaks across each class
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207 * RSD of retention time for grouped peaks across each class
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208 * Coverage across all classes
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209 * mzmin_full & mzmax_full: the full mzrange of each grouped peak
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210 * rtmin_full & rtmax_full: the full rtrange of each grouped peak
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211 * flag for criteria for the blank class (if 1 it means the blank is valid in at least 1 condition) and this grouped peak will be removed
0
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212 * flag for criteria for the sample classes (if 1 it means that this grouped peak is valid for this class)
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213 * all_sample_valid: flag for all samples (if 1 it means that at least 1 sample class is valid, this ignores the blank)
0
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214
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215 To filter out blank peaks just filter out all peaks where the blank_valid is equal to 1
0
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216 This is in addition to the standard output from the xcmsSet peaklist
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217
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218 **flag example**
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219
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220 Dataset consists of 3 classes. Blank, cond1 and cond2. The classes cond1 and cond2 are biological sample classes.
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221
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222 ============= ============= ============= ================ ================
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223 blank_valid cond1_valid cond2_valid all_sample_valid Keep peak?
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224 ============= ============= ============= ================ ================
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225 0 0 1 1 Yes
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226 ------------- ------------- ------------- ---------------- ----------------
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227 0 1 1 1 Yes
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228 ------------- ------------- ------------- ---------------- ----------------
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229 1 0 1 1 No
0
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230 ------------- ------------- ------------- ---------------- ----------------
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231 1 0 0 0 No
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232 ------------- ------------- ------------- ---------------- ----------------
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233 0 0 0 0 No
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234 ============= ============= ============= ================ ================
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235
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236
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237
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238 -----------------
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239 Filters for flags
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240 -----------------
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241
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242 The following filters can be used to determine if a grouped peak gets flagged to keep. If the column all_sample_valid is 0 then
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243 the grouped peak will be removed
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244
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245
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246 * RSD of intensity for each biological sample class
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247 * minfrac for each biological sample class
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248 * RSD of retention time for each biological sample class
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249 * intensity threshold for each biological sample class
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250 * Blank subtraction. If a blank peak is found where the intensity of any corresponding biological sample class is not greater that the he s2b threshold (sample/blank). Then this grouped peak will be flagged for removal
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251
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252 The blank grouped peaks also have there own filters. If the blank peak passes this criteria and s2b threshold detailed above
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253 then the peak will be removed.
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254
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255 * RSD of intensity
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256 * minfrac
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257 * intensity threshold
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258
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259 Additionally there is a filter for assessing how well the peaks fit the gaussian shape. Note that this can only be performed
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260 when XCMS has fit_gauss option and verbose columns set to TRUE. Also, these peaks are just removed and not flagged.
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261
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262
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263
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264 -----------
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265 Regrouping
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266 -----------
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267 The resulting xcmsSet object where all peaks have been removed needs to be regrouped otherwise the individual peaks
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268 associated with each file will not be correctly linked to the grouped peaks.
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269
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270 This tool will re-group the xcmsSet object and check the newly created re-grouped xcmsSet object to see if any peaks are
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271 still being flagged. If so the process will be repeated untill the xcmsSet object only contains peaks that match
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272 the peak criteria.
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273
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274 The output file is an xcmsSet.RData file.
c9d911d33970 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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275 ]]></help>
8
0ccb8c91be19 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit fdaf9fc69c205ed76ef7cd82f4fa1624cf40419b-dirty
tomnl
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276 </tool>