Mercurial > repos > ethevenot > biosigner

annotate biosigner_config.xml @ 3:fa80bd02055f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab
author ethevenot
date Tue, 06 Jun 2017 11:44:00 -0400
parents b2414be87d4b
children
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fa80bd02055f planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab
ethevenot
parents: 2
diff changeset
1 <tool id="biosigner" name="Biosigner" version="2.2.7">
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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2 <description>Molecular signature discovery from omics data</description>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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3
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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4 <requirements>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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5 <requirement type="package">r-batch</requirement>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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6 <requirement type="package">bioconductor-biosigner</requirement>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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7 </requirements>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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9 <stdio>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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10 <exit_code range="1:" level="fatal" />
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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11 </stdio>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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13 <command><![CDATA[
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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14 Rscript $__tool_directory__/biosigner_wrapper.R
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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16 dataMatrix_in "$dataMatrix_in"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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17 sampleMetadata_in "$sampleMetadata_in"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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18 variableMetadata_in "$variableMetadata_in"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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19
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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20 respC "$respC"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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22 #if $advCpt.opcC == "full"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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23 methodC "$advCpt.methodC"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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24 bootI "$advCpt.bootI"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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25 tierC "$advCpt.tierC"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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26 pvalN "$advCpt.pvalN"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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27 seedI "$advCpt.seedI"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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28 #end if
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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29
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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30 variableMetadata_out "$variableMetadata_out"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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31 figure_tier "$figure_tier"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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32 figure_boxplot "$figure_boxplot"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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33 information "$information"
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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34 ]]></command>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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35
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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36 <inputs>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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37 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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38 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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39 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" />
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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40 <param name="respC" label="Sample classes" type="text" value = "" help="Column of sampleMetadata containing 2 types of strings (e.g., 'case' and 'control')" />
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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41
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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42 <conditional name="advCpt">
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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43 <param name="opcC" type="select" label="Advanced computational parameters" >
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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44 <option value="default" selected="true">Use default</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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45 <option value="full">Full parameter list</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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46 </param>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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47 <when value="default"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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48 <when value="full">
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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49 <param name="methodC" label="Classification method(s)" type="select" help="">
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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50 <option value="all" selected="true">all</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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51 <option value="plsda">PLS-DA</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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52 <option value="randomforest">Random Forest</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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53 <option value="svm">SVM</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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54 </param>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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55 <param name="bootI" type="integer" value="50" label="Number of bootstraps" help=""/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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56 <param name="tierC" label="Selection tier(s)" type="select" help="">
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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57 <option value="S" selected="true">S</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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58 <option value="A">S+A</option>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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59 </param>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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60 <param name="pvalN" type="float" value="0.05" label="p-value threshold" help="Must be between 0 and 1"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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61 <param name="seedI" type="integer" value="0" label="Seed" help="Select an integer (e.g., 123) if you want to obtain exactly the same signatures when re-running the algorithm; 0 means that no seed is selected"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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62 </when>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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63 </conditional>
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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64 </inputs>
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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65
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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66 <outputs>
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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67 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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68 <data name="figure_tier" label="${tool.name}__figure-tier.pdf" format="pdf"/>
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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69 <data name="figure_boxplot" label="${tool.name}__figure-boxplot.pdf" format="pdf"/>
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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70 <data name="information" label="${tool.name}__information.txt" format="txt"/>
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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71 </outputs>
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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72
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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73 <tests>
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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74 <test>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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75 <param name="dataMatrix_in" value="dataMatrix.tsv"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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76 <param name="sampleMetadata_in" value="sampleMetadata.tsv"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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77 <param name="variableMetadata_in" value="variableMetadata.tsv"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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78 <param name="respC" value="gender"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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79 <param name="opcC" value="full"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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80 <param name="methodC" value="all"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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81 <param name="bootI" value="5"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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82 <param name="tierC" value="S"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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83 <param name="pvalN" value="0.05"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 1
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84 <param name="seedI" value="123"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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85 <output name="variableMetadata_out" file="variableMetadata.out"/>
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
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86 </test>
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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87 </tests>
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
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88
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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89 <help>
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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90
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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91 .. class:: infomark
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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92
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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93 **Author** Philippe Rinaudo and Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)
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94
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95 ---------------------------------------------------
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96
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97 .. class:: infomark
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98
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99 **Please cite**
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100
2
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101 Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2016). *biosigner*: a new method for the discovery of significant molecular signatures from omics data. *Frontiers in Molecular Biosciences*, **3** (http://dx.doi.org/10.3389/fmolb.2016.00026).
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102
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103 ---------------------------------------------------
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104
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105 .. class:: infomark
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106
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107 **R package**
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108
2
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109 The *biosigner* package is available from the bioconductor repository (http://bioconductor.org/packages/biosigner).
0
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110
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111 ---------------------------------------------------
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112
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113 .. class:: infomark
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114
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115 **Tool updates**
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116
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117 See the **NEWS** section at the bottom of this page
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118
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119 ---------------------------------------------------
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120
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121 ==========================================================
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122 *biosigner*: Molecular signature discovery from omics data
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123 ==========================================================
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124
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125 -----------
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126 Description
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127 -----------
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128
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129 High-throughput, non-targeted, technologies such as transcriptomics, proteomics and metabolomics, are widely used to **discover molecules** which allow to efficiently discriminate between biological or clinical conditions of interest (e.g., disease vs control states). Powerful **machine learning** approaches such as Partial Least Square Discriminant Analysis (PLS-DA), Random Forest (RF) and Support Vector Machines (SVM) have been shown to achieve high levels of prediction accuracy.
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130
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131 **Feature selection**, i.e., the selection of the few features (i.e., the molecular signature) which are of highest discriminating value, is a critical step in building a robust and relevant classifier (Guyon and Elisseeff, 2003): First, dimension reduction is usefull to limit the risk of overfitting and reduce the prediction variability of the model; second, intrepretation of the molecular signature is facilitated; third, in case of the development of diagnostic product, a restricted list is required for the subsequent validation steps (Rifai et al, 2006).
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132
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133 Since the comprehensive analysis of all combinations of features is not computationally tractable, several selection techniques have been described (Saeys et al, 2007). The major challenge for such methods is to be fast and extract **restricted and stable molecular signatures** which still provide high performance of the classifier (Gromski et al, 2014; Determan, 2015).
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134
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135 The **biosigner** module implements a new feature selection algorithm to assess the relevance of the variables for the prediction performances of the classifier (Rinaudo et al, submitted). Three binary classifiers can be run in parallel, namely **PLS-DA**, **Random Forest** and **SVM**, as the performances of each machine learning approach may vary depending on the structure of the dataset. The algorithm computes the *tier* of each feature for the selected classifer(s): tier *S* corresponds to the final signature, i.e., features which have been found significant in all the selection steps; features with tier *A* have been found significant in all but the last selection, and so on for tier *B* to *E*. It returns the **signature** (by default from the *S* tier) for each of the selected classifier as an additional column of the **variableMetadata** table. In addition the *tiers* and **individual boxplots** of the selected features are returned.
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136
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137 The module has been successfully applied to **transcriptomics** and **metabolomics** data.
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138
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139 Note:
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140 | 1) Only **binary** classification is currently available,
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141 | 2) If the **dataMatrix** contains **missing** values (NA), these features will be removed prior to modeling with Random Forest and SVM (in contrast, the NIPALS algorithm from PLS-DA can handle missing values),
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142 | 3) As the algorithm relies on bootstrapping, re-running the module may result in slightly different results. To ensure that returned results are exactly the same, the **seed** (advanced) parameter can be used.
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143 |
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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 .. class:: infomark
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149
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150 **References**
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151
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152 | Determan C. (2015). Optimal algorithm for metabolomics classification and feature selection varies by dataset. International *Journal of Biology* 7, 100-115.
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153 | Gromski P.S., Xu Y., Correa E., Ellis D.I., Turner M.L. and Goodacre R. (2014). A comparative investigation of modern feature selection and classification approaches for the analysis of mass spectrometry data . *Analytica Chimica Acta* 829, 1-8.
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154 | Guyon I. and Elisseeff A. (2003). An introduction to variable and feature selection. *Journal of Machine Learning Research* 3, 1157-1182.
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155 | Rifai N., Gillette M.A. and Carr S.A. (2006). Protein biomarker discovery and validation: the long and uncertain path to clinical utility. *Nature Biotechnology* 24, 971-983.
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156 | Rinaudo P., Junot C. and Thevenot E.A. *biosigner*: A new method for the discovery of restricted and stable molecular signatures from omics data. *submitted*.
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157 | Saeys Y., Inza I. and Larranaga P. (2007). A review of feature selection techniques in bioinformatics. *Bioinformatics* 23, 2507-2517.
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158
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159 ---------------------------------------------------
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160
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161 -----------------
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162 Workflow position
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163 -----------------
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164
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165 .. image:: biosigner_workflowPositionImage.png
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166 :width: 600
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167
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168 -----------
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169 Input files
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170 -----------
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171
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172 +---------------------------+------------+
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173 | File | Format |
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174 +===========================+============+
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175 | 1) Data matrix | tabular |
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176 +---------------------------+------------+
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177 | 2) Sample metadata | tabular |
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178 +---------------------------+------------+
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179 | 3) Variable metadata | tabular |
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180 +---------------------------+------------+
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181
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182
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183 ----------
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184 Parameters
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185 ----------
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186
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187 Data matrix file
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188 | variable x sample **dataMatrix** tabular separated file of the numeric intensities, with . as decimal, and NA for missing values; use the **Check Format** tool in the **LC-MS/Quality Control** section to check the formats of your **dataMatrix**, **sampleMetadata** and **variableMetadata** files
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189 |
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190
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191 Sample metadata file
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192 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values; use the **Check Format** tool in the **LC-MS/Quality Control** section to check the formats of your **dataMatrix**, **sampleMetadata** and **variableMetadata** files
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193 |
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194
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195 Variable metadata file
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196 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values; use the **Check Format** tool in the **LC-MS/Quality Control** section to check the formats of your **dataMatrix**, **sampleMetadata** and **variableMetadata** files
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197 |
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198
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199 Classes of samples
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200 | Column of the sample metadata table to be used as the qualitative **binary** response to be modelled; the column should contain only two types of strings (e.g., 'case' and 'control')
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201 |
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202
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203 Advanced: Classification method(s) (default = all)
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204 | Either one or all of the following classifiers: Partial Least Squares Discriminant Analysis (PLS-DA), or Random Forest, or Support Vector Machine (SVM)
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205 |
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206
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207 Advanced: Number of bootstraps (default = 50)
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208 | This parameter controls the number of times the model performance is compared to the prediction on a test subset where the intensities of the candidate feature have been randomly permuted.
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209 |
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210
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211 Advanced: Selection tier(s) (default = S)
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212 | Tier *S* corresponds to the final signature, i.e., features which have been found significant in all the backward selection steps; features with tier *A* have been found significant in all but the last selection, and so on for tier *B* to *E*. Default selection tier is *S*, meaning that the final signature only is returned; to view a larger number of candidate features, the *S+A* tiers can be selected.
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213 |
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214
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215 Advanced: p-value threshold (default = 0.05)
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216 | This threshold controls the selection of the features at each selection round (tier): to be selected, the proportion of times the prediction on the test set with the randomized intensities of the feature is more accurate than on the original test set must be inferior to this threshold. For example, if the number of bootstraps is 50, no more than 2 out of the 50 predictions on the randomized test set must not be more accurate than on the original test set (since 1/50 = 0.02).
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217
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218 Advanced: Seed (default = 0)
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219 | As the algorithm relies on resampling (bootstrap), re-running the module may result in slightly different signatures. To ensure that returned results are exactly the same, the **seed** parameter (integer) can be used; the default, 0, means that no seed is used.
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220 |
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221
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222 ------------
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223 Output files
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224 ------------
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225
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226 variableMetadata_out.tabular
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227 | When a least one feature has been selected, a **tier** column is added indicating for each feature the classifier(s) it was selected from.
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228 |
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229
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230 figure-tier.pdf
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231 | Graphic summarizing which features were selected, with their corresponding tier (i.e., round(s) of selection) for each classifier.
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232 |
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233
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234 figure-boxplot.pdf
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235 | Individual boxplots of the features which were selected in at least one of the signatures. Features selected for a single classifier are colored (*red* for PLS-DA, *green* for Random Forest, and *blue* for SVM)
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236 |
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237
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238 information.txt
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239 | Text file with all messages and warnings generated during the computation.
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240 |
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241
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242 ---------------------------------------------------
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243
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244 ---------------
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245 Working example
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246 ---------------
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247
2
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248 See the **W4M00001a_sacurine-subset-statistics** and **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
0
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249
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250
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251
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252 Figure output
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253 =============
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254
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255 .. image:: biosigner_workingExampleImage.png
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256 :width: 600
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257
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258 ---------------------------------------------------
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259
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260 ----
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261 NEWS
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262 ----
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263
2
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264 CHANGES IN VERSION 2.2.6
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265 ========================
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266
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267 INTERNAL MODIFICATIONS
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268
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269 Minor internal modifications
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270
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271 CHANGES IN VERSION 2.2.4
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272 ========================
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273
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274 INTERNAL MODIFICATIONS
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275
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276 Creating additional files for planemo and travis running and installation validation
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277
0
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278 CHANGES IN VERSION 2.2.2
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279 ========================
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280
2
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281 INTERNAL MODIFICATIONS
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282
0
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283 Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)
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284
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285 CHANGES IN VERSION 2.2.1
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286 ========================
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287
2
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288 NEW FEATURE
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289
0
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290 Creation of the tool
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291
2
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292 </help>
0
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293
2
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294 <citations>
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295 <citation type="bibtex">@Article{Rinaudo2016,
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296 Title = {biosigner: a new method for the discovery of significant molecular signatures from omics data},
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297 Author = {Rinaudo, Philippe and Boudah, Samia and Junot, Christophe and Thevenot, Etienne A},
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298 Journal = {Frontiers in Molecular Biosciences},
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299 Year = {2016},
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300 Pages = {--},
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301 Volume = {3},
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302 Doi = {10.3389/fmolb.2016.00026}
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303 }</citation>
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304 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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305 </citations>
0
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306
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307 </tool>