Mercurial > repos > tomnl > flag_remove_peaks

annotate flag-remove-peaks.xml @ 4:effabeb7dbd2 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 578fd07833b93847193666c11744ba0bca1aaf57-dirty
author tomnl
date Thu, 03 May 2018 06:44:40 -0400
parents 9c4fabc5f7f9
children 0ccb8c91be19
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1 <tool id="flag_remove_peaks" name="flag_remove_peaks" version="0.1.3">
2
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2 <requirements>
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3 <requirement type="package" >r</requirement>
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4 <requirement type="package" >r-optparse</requirement>
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5 <requirement type="package" version="0.0.3" >r-xcmswrapper</requirement>
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6 </requirements>
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7 <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
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8 (e.g. RSD of intensity and retention time).
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9 </description>
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10
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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14 <command interpreter="Rscript"><![CDATA[
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15 flag-remove-peaks.R
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16 --xset_path=$xset_path
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17
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18 #if $sample_flag.sample_flag=='update'
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19 --rsd_i_sample=$sample_flag.rsd_i_sample
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20 --minfrac_sample=$sample_flag.minfrac_sample
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21 --ithres_sample=$sample_flag.ithres_sample
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22 #end if
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23
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24 #if $blank_flag.blank_flag=='update'
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25 --rsd_i_blank=$blank_flag.rsd_i_blank
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26 --minfrac_blank=$blank_flag.minfrac_blank
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27 --ithres_blank=$blank_flag.ithres_blank
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28 --blank_class=$blank_flag.blank_class
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29 #end if
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30
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31 #if $peak_removal.peak_removal=='remove'
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32 --remove_spectra
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33 --minfrac_xcms=$peak_removal.minfrac_xcms
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34 --mzwid=$peak_removal.mzwid
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35 --bw=$peak_removal.bw
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36 #end if
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37
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38 #if $advanced.advanced=='update'
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39 --egauss_thr=$advanced.egauss_thr
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40 --polarity=$advanced.polarity
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41 --grp_rm_ids=$advanced.grp_rm_ids
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42 --xset_name=$advanced.xset_name
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43 $advanced.temp_save.value
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44
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45 #end if
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46 ]]></command>
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47 <inputs>
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48 <param type="data" name="xset_path"
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49 help="The path to the xcmsSet object saved as an RData file"/>
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50 <conditional name="sample_flag">
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51 <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
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52 <option value="update" >Update biological sample flag parameters</option>
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53 <option value="" selected="true">Use default biological sample flag parameters</option>
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54 </param>
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55 <when value="">
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56 </when>
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57 <when value="update">
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58 <param name="rsd_i_sample" type="text" label="rsd_i_sample" value="NA"
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59 help="Relative Standard Deviation threshold for the sample classes (--rsd_i_sample)"/>
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60 <param name="minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1"
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61 help="minimum fraction of files for features needed for the sample classes (--minfrac_sample)"/>
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62 <param name="rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA"
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63 help="Relative standard Deviation threshold for the retention time of the sample
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64 classes (--rsd_rt_sample)"/>
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65 <param name="ithres_sample" type="text" label="ithres_sample" value="NA"
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66 help="Intensity threshold for the sample (--ithres_sample)"/>
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67 </when>
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68 </conditional>
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69 <conditional name="blank_flag">
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70 <param name="blank_flag" type="select" label="Change blank flag parameters?">
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71 <option value="update" >Update blank flag parameters</option>
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72 <option value="" selected="true">Use default blank flag parameters</option>
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73 </param>
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74 <when value="">
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75 </when>
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76 <when value="update">
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77 <param name="blank_class" type="text" label="blank_class" value="blank"
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78 help="A string representing the class that will be used for the blank (--blank_class)"/>
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79 <param name="rsd_i_blank" type="text" label="rsd_i_blank" value="NA"
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80 help="RSD threshold for the blank (--rsd_i_blank)"/>
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81 <param name="minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1"
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82 help="minimum fraction of files for features needed for the blank (--minfrac_blank)"/>
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83 <param name="rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA"
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84 help="RSD threshold for the retention time of the blank (--rsd_rt_blank)"/>
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85 <param name="ithres_blank" type="text" label="ithres_blank" value="NA"
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86 help="Intensity threshold for the blank (--ithres_blank)"/>
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87 <param name="s2b" type="float" label="s2b" value="10"
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88 help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
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89 if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
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90 1000/10 = 100, so sample has fold change higher than the threshold and the peak
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91 is not considered a blank (--s2b)"/>
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92 </when>
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93 </conditional>
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94 <conditional name="peak_removal">
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95 <param name="peak_removal" type="select" label="Remove peaks from xcmsSet object?">
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96 <option value="remove" >Remove peaks and re-group</option>
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97 <option value="" selected="true">Only flag peaks (do not remove and re-group)</option>
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98 </param>
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99 <when value="">
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100 </when>
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101 <when value="remove">
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102 <param name="minfrac_xcms" type="float" label="minfrac_xcms" value="0.5" min="0.0" max="1"
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103 help="minfrac for xcms grouping (--minfrac_xcms)"/>
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104 <param name="mzwid" type="float" label="mzwid" value="0.001"
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105 help="mzwid for xcms grouping (--minfrac_xcms)"/>
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106 <param name="bw" type="float" label="bw" value="5"
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107 help="bw for xcms grouping(--minfrac_xcms)"/>
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108 </when>
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109 </conditional>
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110 <conditional name="advanced">
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111 <param name="advanced" type="select" label="Advanced parameters">
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112 <option value="update" >Update advanced and testing parameters</option>
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113 <option value="" selected="true">Use default advanced parameters</option>
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114 </param>
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115 <when value="">
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116 </when>
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117 <when value="update">
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118 <param name="egauss_thr" type="text" label="egauss_thr" value="NA"
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119 help="Threshold for filtering out non gaussian shaped peaks. Note this only works
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120 if the 'verbose columns' and 'fit gauss' was used with xcms (--egauss_thr)"/>
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121 <param name="temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue=""
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122 help="Assign True if files for each step saved (for testing purposes) (--temp_save)"/>
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123 <param name="polarity" type="select" label="polarity"
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124 help="polarity (just used for naming purpose when files are saved) (--polarity)">
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125 <option value="positive">Positive</option>
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126 <option value="negative" >Negative</option>
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127 <option value="NA" selected="true">NA</option>
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128 </param>
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129 <param name="grp_rm_ids" type="text" label="grp_rm_ids" value="NA"
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130 help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output)
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131 e.g '1,20,30,56'
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132 (--grp_rm_ids)"/>
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133 <param name="xset_name" type="text" label="xset_name" value="xset"
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134 help="Name of the xcmsSet object within the RData file (--xset_name)"/>
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135
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136 </when>
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137 </conditional>
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138 </inputs>
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139 <outputs>
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140 <data name="peaklist_filtered" format="tabular" label="peaklist_filtered"
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141 from_work_dir="peaklist_filtered.txt" visible="true"/>
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142 <data name="removed_peaks" format="tabular" label="removed_peaks"
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143 from_work_dir="removed_peaks.txt" visible="true"/>
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144 <data name="xset_filtered" format="rdata" label="xset_filtered"
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145 from_work_dir="xset_filtered.RData" visible="true"/>
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146 </outputs>
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147 <tests>
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148 <test>
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149 <param name="blank_flag.blank_flag" value="update" />
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150 <conditional name="blank_flag">
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151 <param name="blank_flag" value="update"/>
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152 <param name="blank_class" value="KO" />
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153 </conditional>
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154 <conditional name="peak_removal">
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155 <param name="peak_removal" value="remove"/>
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156 </conditional>
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157 <param name="xset_path" value="xset.RData" type="rdata" />
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158 <output name="peaklist_filtered" type="tabular" file="peaklist_filtered.tabular">
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159 </output>
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160 <output name="removed_peaks" type="tabular" file="removed_peaks.tabular">
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161 </output>
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162
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163
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164 </test>
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165 </tests>
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166 <help><![CDATA[
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167
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168 =======================================
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169 Flag & remove peaks from xcmsSet object
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170 =======================================
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171 -----------
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172 Description
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173 -----------
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174
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175 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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176 completely from the xcmsSet object (xset). This means removing the individual peaks associated for each file. Located
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177 in the **xset@peaks** socket of the xcmsSet object.
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178
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179 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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180 be removed.
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181
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182 **Note**: grouped peak refers to a peak that has been grouped together by xcms::group function
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183
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184 -----------------
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185 Updated peaklist
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186 -----------------
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187 The calculated columns for the update peaklist dataframe include:
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188
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189 * RSD of intensity for grouped peaks across each class
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190 * RSD of retention time for grouped peaks across each class
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191 * Coverage across all classes
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192 * mzmin_full & mzmax_full: the full mzrange of each grouped peak
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193 * rtmin_full & rtmax_full: the full rtrange of each grouped peak
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194 * flag for criteria for the blank class (if 1 it means the blank is valid) and this grouped peak will be removed
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195 * flag for criteria for the sample classes (if 1 it means that this grouped peak is valid for this class)
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196 * all_sample_valid: flag for all samples (if 1 it means that at least 1 sample class is valid and the blank is not valid) (we keep the grouped peak)
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197
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198 This is in addition to the standard output from the xcmsSet peaklist
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199
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200 **flag example**
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201
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202 Dataset consists of 3 classes. Blank, cond1 and cond2. The classes cond1 and cond2 are biological sample classes.
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203
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204 ============= ============= ============= ================ ================
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205 blank_valid cond1_valid cond2_valid all_sample_valid Keep peak?
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206 ============= ============= ============= ================ ================
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207 0 0 1 1 Yes
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208 ------------- ------------- ------------- ---------------- ----------------
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209 0 1 1 1 Yes
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210 ------------- ------------- ------------- ---------------- ----------------
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211 1 0 1 0 No
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212 ------------- ------------- ------------- ---------------- ----------------
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213 1 0 0 0 No
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214 ------------- ------------- ------------- ---------------- ----------------
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215 0 0 0 0 No
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216 ============= ============= ============= ================ ================
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217
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218
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219
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220 -----------------
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221 Filters for flags
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222 -----------------
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223
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224 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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225 the grouped peak will be removed
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226
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227
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228 * RSD of intensity for each biological sample class
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229 * minfrac for each biological sample class
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230 * RSD of retention time for each biological sample class
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231 * intensity threshold for each biological sample class
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232 * 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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233
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234 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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235 then the peak will be removed.
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236
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237 * RSD of intensity
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238 * minfrac
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239 * intensity threshold
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240
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241 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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242 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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243
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244
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245
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246 -----------
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247 Regrouping
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248 -----------
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249 The resulting xcmsSet object where all peaks have been removed needs to be regrouped otherwise the individual peaks
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250 associated with each file will not be correctly linked to the grouped peaks.
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251
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252 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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253 still being flagged. If so the process will be repeated untill the xcmsSet object only contains peaks that match
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254 the peak criteria.
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255
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256 The output file is an xcmsSet.RData file.
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257 ]]></help>
2
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258 </tool>