Mercurial > repos > workflow4metabolomics > camera_groupcorr

annotate groupCorr.xml @ 0:cb57be5de070 draft default tip

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planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
author workflow4metabolomics
date Sun, 24 Nov 2024 21:29:48 +0000
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1 <tool id="CAMERA_groupCorr" name="CAMERA.groupCorr" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0">
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2
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3 <description>EIC correlation grouping of LC/ESI-MS data</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
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11 <required_files>
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12 <include type="literal" path="CAMERA_groupCorr.R"/>
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13 <include type="literal" path="lib.r"/>
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14 </required_files>
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15
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16 <command detect_errors="exit_code"><![CDATA[
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17 @COMMAND_RSCRIPT@CAMERA_groupCorr.R
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18 image '$image'
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19 cor_eic_th $cor_eic_th
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20 pval $pval
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21 graphMethod $graphMethod
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22 calcIso $calcIso
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23 calcCiS $calcCiS
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24 calcCaS $calcCaS
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25
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26 #if $psg_list_block.psg_list_select == "FALSE":
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27 psg_list NULL
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28 #else
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29 psg_list $psg_list
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30 #end if
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31
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32 cor_exp_th $cor_exp_th
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33 intval $intval
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34 numDigitsMZ $numDigitsMZ
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35 numDigitsRT $numDigitsRT
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36 convertRTMinute $convertRTMinute
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37
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38 @COMMAND_FILE_LOAD@
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39 ]]>
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40 </command>
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41
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42 <inputs>
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43 <param name="image" type="data" label="RData file" format="rdata" help="output file from another function xcms (fillPeaks)" />
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44 <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="Correlation threshold (0..1)" />
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45 <param name="pval" type="float" value="0.05" max="1" min="0" label="Significant correlation threshold" />
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46 <param name="graphMethod" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
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47 <option value="hcs" selected="true">hcs</option>
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48 <option value="lpc">lpc</option>
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49 </param>
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50 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use isotopic relationship for peak grouping" />
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51 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use correlation inside samples for peak grouping" />
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52 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use correlation across samples for peak grouping" />
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53 <param name="cor_exp_th" type="float" value="0.75" max="1" min="0" label="Threshold for intensity correlations across samples (0..1)" />
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54 <param name="intval" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra">
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55 <option value="into" selected="true">into</option>
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56 <option value="maxo">maxo</option>
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57 <option value="intb">intb</option>
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58 <!-- <option value="intf">intf</option>
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59 <option value="maxf">maxf</option>
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60 <option value="area">area</option> -->
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61 </param>
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62 <conditional name="psg_list_block">
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63 <param name="psg_list_select" type="select" label="Use a personal psg_list">
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64 <option value="TRUE">TRUE</option>
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65 <option value="FALSE" selected="true">FALSE</option>
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66 </param>
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67 <when value="FALSE">
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68 <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />-->
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69 </when>
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70 <when value="TRUE">
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71 <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." />
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72 </when>
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73 </conditional>
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74 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" />
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75 <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" />
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76 <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" />
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77 <expand macro="input_file_load"/>
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78 </inputs>
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79 <outputs>
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80 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.groupCorr.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
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81 <data name="camera_groupCorr_rdata" format="rdata" label="${image.name[:-6]}.groupCorr.RData" from_work_dir="camera_groupCorr.RData" />
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82 </outputs>
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83 <tests>
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84 <test expect_num_outputs="2">
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85 <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.RData" />
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86 <!--<param name="cor_eic_th" value="0.75" />
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87 <param name="pval" value="0.05" />
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88 <param name="graphMethod" value="hcs" />
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89 <param name="calcIso" value="FALSE" />
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90 <param name="calcCiS" value="TRUE" />
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91 <param name="calcCaS" value="FALSE" />
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92 <param name="cor_exp_th" value="0.75" />
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93 <param name="intval" value="into" />-->
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94 <expand macro="test_file_load_faahKO_15"/>
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95 <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.variableMetadata.tsv" />
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96 <output name="camera_groupCorr_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.RData" compare="sim_size" delta="5000" />
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100
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101 ================
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102 CAMERA.groupCorr
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103 ================
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104
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105 -----------
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106 Description
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107 -----------
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108
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109 .. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf
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110
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111 Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object.
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112 Return an xsAnnotate object with grouping information. Click on the link to see the "Reference Manual" : link_ .
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113
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114 ---------------------------------------------------
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115
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116 ---------
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117 Arguments
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118 ---------
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119
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120 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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121 | Variables | Descriptions |
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122 +================+=============================================================================================================================================+
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123 | object | the xsAnnotate object |
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124 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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125 | cor_eic_th | Correlation threshold for EIC correlation |
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126 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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127 | pval | p-value threshold for testing correlation of significance |
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128 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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129 | graphMethod | Clustering method for resulting correlation graph. See calcPC for more details. |
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130 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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131 | calcIso | Include isotope detection information for graph clustering |
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132 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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133 | calcCiS | Calculate correlation inside samples |
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134 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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135 | calcCaS | Calculate correlation across samples |
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136 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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137 | psg_list | Vector of pseudospectra indices. The correlation analysis will be only done for those groups |
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138 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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139 | xraw | Optional xcmsRaw object, which should be used for raw data extraction |
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140 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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141 | cor_exp_th | Threshold for intensity correlations across samples |
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142 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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143 | intval | Selection of the intensity values (such as "into") that should be used in the correlation analysis. See getPeaklist for all allowed values. |
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144 +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+
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145
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146 ---------------------------------------------------
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147
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148 ------------------------------------------
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149 General schema of the metabolomic workflow
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150 ------------------------------------------
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151
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152 .. image:: groupCorr.png
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153
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154 ---------------------------------------------------
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155
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156 -------
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157 Details
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158 -------
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159
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160 The algorithm calculates different informations for group peaks into so called pseudospectra. This pseudospectra contains peaks, with have a high correlation between each other. So far three different kind of information are available. Correlation of intensities across samples (need more than 3 samples), EIC correlation between peaks inside a sample and additional the informationen about recognized isotope cluster can be included. After calculation of all these informations, they are combined as edge value into a graph object. A following graph clustering algorithm separate the peaks (nodes in the graph) into the pseudospectra.
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161
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162 ---------------------------------------------------
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163
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164 --------------
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165 Changelog/News
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166 --------------
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167
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168 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
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169
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170 @HELP_CAMERA_SUITE@
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171
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172 ]]> </help>
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173
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174 <expand macro="citation"/>
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175 <expand macro="creator"/>
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176 </tool>