Mercurial > repos > marie-tremblay-metatoul > asca
annotate asca_xml.xml @ 0:93312041f1d5 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
author | marie-tremblay-metatoul |
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date | Fri, 21 Sep 2018 05:51:14 -0400 |
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93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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1 <tool id="asca" name="ASCA" version="1.0.0"> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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2 <description>Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block</description> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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3 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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4 <requirements> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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5 <requirement type="package" version="1.1_4">r-batch</requirement> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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6 <requirement type="package" version="1.0">r-MetStaT</requirement> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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7 <requirement type="package" version="1.70.0">bioconductor-pcamethods</requirement> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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8 </requirements> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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9 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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10 <stdio> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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11 <exit_code range="1:" level="fatal" /> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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12 </stdio> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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13 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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14 <command><![CDATA[ |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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15 Rscript $__tool_directory__/asca_wrapper.R |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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16 dataMatrix_in "$dataMatrix_in" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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17 sampleMetadata_in "$sampleMetadata_in" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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18 variableMetadata_in "$variableMetadata_in" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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19 factor1 "$factor1" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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20 factor2 "$factor2" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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21 scaling "$scaling" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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22 nPerm "$nPerm" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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23 threshold "$threshold" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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24 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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25 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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26 sampleMetadata_out "$sampleMetadata_out" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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27 variableMetadata_out "$variableMetadata_out" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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28 figure "$figure" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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29 information "$information" |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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30 ]]></command> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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31 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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32 <inputs> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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33 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" /> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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34 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" /> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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35 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" /> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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36 <param name="factor1" label="Name of the sampleMetadata column containing the 1st factor for A-SCA" type="text" value="none" help=""/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
changeset
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37 <param name="factor2" label="Name of the sampleMetadata column containing the 2nd factor for A-SCA" type="text" value="none" help=""/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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38 <param name="scaling" label="Scaling to apply to dataMatrix" type="select" help=""> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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39 <option value="none" selected="true">None</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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40 <option value="pareto">pareto</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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41 <option value="uv">uv</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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42 </param> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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43 <param name="nPerm" label="Number of permutation to perform to compute factor significance" type="select" help=""> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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44 <option value="100" selected="true">100</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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45 <option value="500">500</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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46 <option value="1000">1000</option> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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47 </param> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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48 <param name="threshold" type="float" value="0.05" label="Threshold for factor significance (permutation test)" help="Must be between 0 and 1"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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49 </inputs> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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50 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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51 <outputs> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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52 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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53 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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54 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
diff
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55 <data name="information" label="${tool.name}_information.txt" format="txt"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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56 </outputs> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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57 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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58 <tests> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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59 <test> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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60 <param name="dataMatrix_in" value="choo_datamatrix.txt"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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61 <param name="sampleMetadata_in" value="choo_samplemetadata.txt"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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62 <param name="variableMetadata_in" value="choo_variablemetadata.txt"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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63 <param name="factor1" value="Date"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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64 <param name="factor2" value="Treatment"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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65 <param name="scaling" value="pareto"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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66 <param name="threshold" value="0.05"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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67 <param name="nPerm" value="1000"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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68 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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69 <output name="sampleMetadata_out" file="ASCA_choo_samplemetadata.tsv" lines_diff="6"/> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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70 </test> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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71 </tests> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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72 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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73 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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74 <help> |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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75 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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76 .. class:: infomark |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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77 |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
parents:
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78 **Tool updates** |
93312041f1d5
planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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79 |
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80 See the **NEWS** section at the bottom of this page |
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81 |
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82 --------------------------------------------------- |
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83 |
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84 .. class:: infomark |
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85 |
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86 **Authors** Marie Tremblay-Franco (W4M Core Development Team, MetaboHUB Toulouse, AXIOM) and Yann Guitton (W4M Core Development Team, Laberca, UM1329) |
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87 |
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88 --------------------------------------------------- |
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89 |
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90 .. class:: infomark |
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91 |
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92 **References** |
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93 | R Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (http://www.r-project.org) |
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94 | Tim Dorscheidt (2013). MetStaT: Statistical metabolomics tools. R package version 1.0. https://CRAN.R-project.org/package=MetStaT |
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95 | |
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96 |
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97 ============ |
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98 A-SCA |
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99 ============ |
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100 |
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101 ----------- |
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102 Description |
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103 ----------- |
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104 |
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105 | ASCA splits variance into independent blocks according to the experimental factors and performs multivariate analysis (SCA) of each block |
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106 | |
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107 |
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108 ----------------- |
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109 Workflow position |
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110 ----------------- |
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111 |
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112 .. image:: images/asca_workflowPositionImage.png |
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113 :width: 600 |
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114 |
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115 |
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116 ----------- |
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117 Input files |
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118 ----------- |
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119 |
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120 +----------------------------+---------+ |
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121 | Parameter : num + label | Format | |
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122 +============================+=========+ |
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123 | 1 : Data matrix file | tabular | |
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124 +----------------------------+---------+ |
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125 | 2 : Sample metadata file | tabular | |
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126 +----------------------------+---------+ |
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127 | 3 : Variable metadata file | tabular | |
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128 +----------------------------+---------+ |
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129 |
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130 |
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131 | The **required formats** for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org (http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf) |
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132 |
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133 |
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134 ---------- |
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135 Parameters |
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136 ---------- |
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137 |
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138 Data matrix file |
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139 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below) |
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140 | |
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141 |
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142 Sample metadata file |
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143 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values |
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144 | |
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145 |
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146 Variable metadata file |
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147 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values |
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148 | |
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149 |
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150 Factor1 |
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151 | Name of the sampleMetadata column containing the 1st factor for A-SCA |
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152 | |
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153 |
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154 Factor2 |
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155 | Name of the sampleMetadata column containing the 2nd factor for A-SCA |
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156 | |
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157 |
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158 Scaling (default = none) |
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159 | Mean-centering followed either by pareto scaling (**pareto**), or unit-variance scaling (**UV**) |
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160 | |
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161 |
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162 Permutation testing for A-SCA parameters: Number of permutations (default = 100) |
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163 | Number of random permutation on the results from ASCA. Calculate by repeating the ASCA analysis many times with permutated samples. |
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164 | |
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165 |
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166 Threshold |
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167 | p-value significance threshold for permutation test |
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168 | |
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169 |
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170 ------------ |
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171 Output files |
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172 ------------ |
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173 |
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174 sampleMetadata_out.tabular |
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175 | sampleMetadata data file; may be identical to the input sampleMetadata in case no renaming of sample names nor re-ordering of samples (see the 'information' file for the presence/absence of modifications) |
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176 | |
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177 |
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178 variableMetadata_out.tabular |
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179 | variableMetadata data file; may be identical to the input variableMetadata in case no renaming of variable names nor re-ordering of variables (see the 'information' file for the presence/absence of modifications) |
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180 | |
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181 |
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182 figure.pdf |
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183 | Scree and score plots for significant parameter(s) |
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184 | |
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185 |
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186 information.txt |
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187 | Text file with all messages when error(s) in formats are detected |
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188 | |
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189 |
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190 --------------------------------------------------- |
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191 |
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192 --------------- |
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193 Working example |
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194 --------------- |
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195 |
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196 .. class:: infomark |
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197 |
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198 | Data used in the following example comes from the Biosystems Data Analysis Group. They ayre included in the ASCA software(http://www.bdagroup.nl/content/Downloads/software/software.php). |
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199 | Two features were measured on 12 individuals, using a two factor-experimental design. The 1st factor has 2 levels and the 2nd factor has 3 levels. |
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200 | |
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201 |
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202 Input files |
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203 ----------- |
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204 +---------------------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+ |
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205 | Datamatrix | Ind1 | Ind2 | Ind3 | Ind4 | Ind5 | Ind6 | Ind7 | Ind8 | Ind9 | Ind10 | Ind11 | Ind12 | |
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206 +=====================+==========+==========+==========+==========+==========+==========+==========+==========+==========+==========+==========+==========+ |
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207 | V1 | 1.00 | 3.00 | 2.00 | 1.00 | 2.00 | 2.00 | 4.00 | 6.00 | 5.00 | 5.00 | 6.00 | 5.00 | |
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208 +---------------------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+ |
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209 | V2 | 0.60 | 0.40 | 0.70 | 0.80 | 0.01 | 0.80 | 1.00 | 2.00 | 0.90 | 1.00 | 2.00 | 0.70 | |
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210 +---------------------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+----------+ |
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211 |
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212 --------------------------------------------------- |
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213 |
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214 +--------------------+----------+----------+ |
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215 | sampleMetadata | F1 | F2 | |
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216 +====================+==========+==========+ |
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217 | Ind1 | 1 | 1 | |
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218 +--------------------+----------+----------+ |
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219 | Ind2 | 1 | 1 | |
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220 +--------------------+----------+----------+ |
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221 | Ind3 | 1 | 2 | |
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222 +--------------------+----------+----------+ |
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223 | Ind4 | 1 | 2 | |
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224 +--------------------+----------+----------+ |
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225 | Ind5 | 1 | 3 | |
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226 +--------------------+----------+----------+ |
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227 | Ind6 | 1 | 3 | |
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228 +--------------------+----------+----------+ |
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229 | Ind7 | 2 | 1 | |
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230 +--------------------+----------+----------+ |
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231 | Ind8 | 2 | 1 | |
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232 +--------------------+----------+----------+ |
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233 | Ind9 | 2 | 2 | |
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234 +--------------------+----------+----------+ |
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235 | Ind10 | 2 | 2 | |
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236 +--------------------+----------+----------+ |
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237 | Ind11 | 2 | 3 | |
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238 +--------------------+----------+----------+ |
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239 | Ind11 | 2 | 3 | |
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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 | Variablemetadata | Number | |
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246 +====================+==========+ |
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247 | V1 | 1 | |
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248 +--------------------+----------+ |
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249 | V2 | 2 | |
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250 +--------------------+----------+ |
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251 |
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252 --------------------------------------------------- |
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253 |
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254 Parameters |
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255 ---------- |
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256 | Name of the sampleMetadata column containing the 1st factor for A-SCA: F1 |
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257 | Name of the sampleMetadata column containing the 2nd factor for A-SCA: F2 |
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258 | Scaling to apply to dataMatrix: none |
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259 | Number of permutation to perform to compute factor significance: 500 |
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260 | Threshold for factor significance (permutation test): 0.05 |
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261 | |
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262 |
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263 Output files |
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264 ------------ |
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265 | **1) Example of a ASCA_BDAGroup_ASCA_samplemetadata.tsv: tsv file** including PC1 and PC2 scores from F1 PCA, F2 PCA and F1xF2 PCA |
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266 |
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267 |
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268 |
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269 +--------------------+----------+----------+-------------+-------------+-------------+-------------+-------------------+-------------------+ |
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270 | sampleMetadata | F1 | F2 | F1_XSCOR-p1 | F1_XSCOR-p2 | F2_XSCOR-p1 | F2_XSCOR-p2 | Interact_XSCOR-p1 | Interact_XSCOR-p1 | |
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271 +====================+==========+==========+=============+=============+=============+=============+===================+===================+ |
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272 | Ind1 | 1 | 1 | -2.66136390 | 0.307505352 | 0.986520075 | -0.25138715 | -0.31885686 | -0.77109078 | |
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273 +--------------------+----------+----------+-------------+-------------+-------------+-------------+-------------------+-------------------+ |
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274 | Ind2 | 1 | 1 | -0.74779084 | -0.30750535 | -0.99758505 | 0.070057773 | 0.719240017 | 0.950058502 | |
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275 +--------------------+----------+----------+-------------+-------------+-------------+-------------+-------------------+-------------------+ |
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276 | Ind3 | 1 | 2 | -1.22618411 | -0.15375267 | -0.24288670 | 0.124191016 | -0.00883820 | 0.465391498 | |
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277 +--------------------+----------+----------+-------------+-------------+-------------+-------------+-------------------+-------------------+ |
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278 |
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279 |
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280 |
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281 | **2) Example of a ASCA_BDAGroup_ASCA_variablemetadata.tsv: tsv file** including PC1 and PC2 loadings from F1 PCA, F2 PCA and F1xF2 PCA |
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282 |
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283 |
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284 +--------------------+----------+-------------+-------------+-------------+-------------+-------------------+--------------------+ |
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285 | variableMetadata | Number | F1_XLOAD-p1 | F1_XLOAD-p2 | F2_XLOAD-p1 | F2_XLOAD-p2 | Interact_XLOAD-p1 | Interact_XLOAD-p1 | |
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286 +====================+==========+=============+=============+=============+=============+===================+====================+ |
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287 | V1 | 1 | 0.977759467 | -0.20972940 | -0.99814337 | 0.060908126 | 0.428703939 | 0.903445035 | |
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288 +--------------------+----------+-------------+-------------+-------------+-------------+-------------------+--------------------+ |
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289 | V2 | 2 | 0.977759467 | -0.30750535 | -0.06090812 | -0.99814337 | -0.90344503 | 0.428703939 | |
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290 +--------------------+----------+-------------+-------------+-------------+-------------+-------------------+--------------------+ |
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291 |
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292 |
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293 |
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294 | **3) Example of a ASCA_information.txt: txt file** including % of explained variance and p-value of permutation test |
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295 |
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296 |
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297 +----------------------+-------------------------+---------------------+ |
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298 | ASCA_information.txt | % of explained variance | Permutation p-value | |
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299 +======================+=========================+=====================+ |
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300 | F1 | 81.71 | 0.004 | |
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301 +----------------------+-------------------------+---------------------+ |
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302 | F2 | 1.29 | 0.880 | |
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303 +----------------------+-------------------------+---------------------+ |
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304 | Interaction | 1.33 | 0.962 | |
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305 +----------------------+-------------------------+---------------------+ |
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306 | Residuals | 15.67 | - | |
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307 +----------------------+-------------------------+---------------------+ |
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308 |
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309 |
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310 | **4) Example of ASCA_figure.pdf: pdf file** including Scree, Score plot and barplot of leverage values only for significant factor(s)/interaction** |
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311 | Leverage: importance of a variable in the PCA model (Nueda et al. 2007) |
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312 |
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313 |
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314 .. image:: BDAGroup_ASCA_figure.tif |
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315 :width: 600 |
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316 |
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317 ---- |
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318 NEWS |
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319 ---- |
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320 |
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321 |
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322 </help> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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323 |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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324 <citations> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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325 <citation type="doi">10.1093/bioinformatics/bti476</citation> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
marie-tremblay-metatoul
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326 <citation type="doi">10.1002/cem.952</citation> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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327 <citation type="doi">10.1093/bioinformatics/btm251</citation> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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328 </citations> |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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329 |
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planemo upload for repository https://github.com/workflow4metabolomics/ascaw4m commit 7ea9b0f8abc5a60c2c04fd2098788497f14766b6
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330 </tool> |