Mercurial > repos > iuc > dimet_pca_analysis
annotate dimet_pca_analysis.xml @ 1:a01453baaf5e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 7568e92bfc4560d6e0287e7444455f55c86d135d
author | iuc |
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date | Tue, 23 Jan 2024 14:57:12 +0000 |
parents | 04d213632103 |
children | c0103ea608fc |
rev | line source |
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04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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1 <tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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2 <description> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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3 Principal Component Analysis for tracer metabolomics data, producing tables (by DIMet) |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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4 </description> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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5 <macros> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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6 <token name="@TOOL_LABEL@">pca analysis</token> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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7 <token name="@EXECUTABLE@">pca_analysis</token> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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8 <import>macros.xml</import> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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9 </macros> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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10 <expand macro="requirements"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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11 <command detect_errors="exit_code"><![CDATA[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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12 @INIT_CONFIG@ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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13 @INIT_PCA@ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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14 @INIT_IMPUTE_VALUES@ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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15 @INIT_CONDITIONS@ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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16 HYDRA_FULL_ERROR=1 python -m dimet |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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17 -cp '$__new_file_path__/config' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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18 '++hydra.run.dir=pca-analysis-tables' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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19 '++figure_path=figures' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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changeset
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20 '++table_path=tables' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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21 '++analysis={ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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22 dataset:{ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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changeset
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23 _target_:dimet.data.DatasetConfig, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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24 name: "Galaxy DIMet run" |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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25 }, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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26 method:{ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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27 _target_: dimet.method.PcaAnalysisConfig, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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28 label: pca-analysis-tables, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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29 name: "Generate Principal Component Analysis tables", |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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30 pca_split_further:['timepoint'], |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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31 draw_ellipses: null, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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32 run_iris_demo: false, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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33 impute_values:${impute_values} |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
parents:
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34 }, |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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35 label: pca-table |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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36 }' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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37 '++analysis.dataset.subfolder=' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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38 '++analysis.dataset.label=' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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39 '++analysis.dataset.conditions=${conds}' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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40 #if $metadata_path: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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41 '++analysis.dataset.metadata=metadata' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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42 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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43 #if $abundance_file: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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44 '++analysis.dataset.abundances=abundance' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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45 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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46 #if $me_or_frac_contrib_file: |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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47 '++analysis.dataset.mean_enrichment=me_or_frac_contrib' |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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48 #end if |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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49 @REMOVE_CONFIG@ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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50 ]]></command> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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51 <inputs> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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52 <expand macro="input_parameters_pca"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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53 <expand macro="conditions"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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54 </inputs> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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55 |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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56 <outputs> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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57 <collection name="report" type="list"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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58 <discover_datasets pattern="__designation__" directory="tables" format="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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59 </collection> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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60 </outputs> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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61 <tests> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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62 <test> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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63 <param name="abundance_file" ftype="tabular" value="rawAbundances.csv" /> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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64 <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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65 <param name="conditions" value='Control,L-Cycloserine'/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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66 <output_collection name="report" type="list" count="12"> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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67 <element file="abundances--cell_pc.csv" name="abundances--cell_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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68 <element file="abundances--cell_var.csv" name="abundances--cell_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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69 <element file="abundances--med_pc.csv" name="abundances--med_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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70 <element file="abundances--med_var.csv" name="abundances--med_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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71 <element file="abundances--T0--cell_pc.csv" name="abundances--T0--cell_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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72 <element file="abundances--T0--cell_var.csv" name="abundances--T0--cell_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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73 <element file="abundances--T0--med_pc.csv" name="abundances--T0--med_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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74 <element file="abundances--T0--med_var.csv" name="abundances--T0--med_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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75 <element file="abundances--T2h--cell_pc.csv" name="abundances--T2h--cell_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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76 <element file="abundances--T2h--cell_var.csv" name="abundances--T2h--cell_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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77 <element file="abundances--T2h--med_pc.csv" name="abundances--T2h--med_pc.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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78 <element file="abundances--T2h--med_var.csv" name="abundances--T2h--med_var.csv" ftype="tabular"/> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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79 </output_collection> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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80 </test> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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81 </tests> |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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82 <help><![CDATA[ |
04d213632103
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0
iuc
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83 This module is part of DIMet: Differential analysis of Isotope-labeled targeted Metabolomics data (https://pypi.org/project/DIMet/). |
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84 |
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85 This tool performs the Principal Components Analysis (PCA) on your data, |
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86 generating the tab-delimited .csv files with the results of the PCA, it is, all the principal components or "dimensions" eigenvalues, and the percentage of explained variances across all the principal components detected in your data. |
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87 |
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88 For automatic plotting of a PCA analysis use our tool **DIMet pca plot** |
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89 |
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90 **Input data files** |
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91 |
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92 This tool requires (at max.) 3 tab-delimited .csv files as inputs. There are two types of files: |
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93 |
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94 - The measures' (or quantifications') files, that can be of 4 types. |
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95 |
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96 - The metadata, a unique file with the description of the samples in your measures' files. This is compulsory. |
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97 |
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98 For running DIMet @EXECUTABLE@ you need **at least one file** of measures: |
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99 |
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100 - The total **abundances** (of the metabolites) file |
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101 |
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102 - The mean **enrichment** or labelled fractional contributions |
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103 |
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104 |
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105 and one metadata file, WHICH IS COMPULSORY, see section **Metadata File Information**. |
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106 |
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107 |
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108 **Measures' files** |
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109 |
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110 The measure's files must be organized as matrices: |
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111 |
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112 - The first column must contain Metabolite IDs that are unique (not repeated) within the file. |
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113 |
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114 - The rest of the columns correspond to the samples |
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115 |
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116 - The rows correspond to the metabolites |
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117 |
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118 - The values must be tab separated, with the first row containing the sample/column labels. |
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119 |
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120 See the following examples of measures files: |
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121 |
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122 |
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123 Example - Metabolites **abundances**: |
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124 |
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125 =============== ================== ================== ================== ================== ================== ================== |
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126 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** |
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127 =============== ================== ================== ================== ================== ================== ================== |
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128 2_3-PG 8698823.9926 10718737.7217 10724373.9 8536484.5 22060650 28898956 |
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129 2-OHGLu 36924336 424336 92060650 45165 84951950 965165051 |
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130 Glc6P 2310 2142 2683 1683 012532068 1252172 |
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131 Gly3P 399298 991656565 525195 6365231 89451625 4952651963 |
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132 IsoCit 0 0 0 84915613 856236 954651610 |
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133 =============== ================== ================== ================== ================== ================== ================== |
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134 |
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135 Example - mean **enrichment** or labeled fractional contributions: |
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136 |
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137 =============== ================== ================== ================== ================== ================== ================== |
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138 ID **MCF001089_TD01** **MCF001089_TD02** **MCF001089_TD03** **MCF001089_TD04** **MCF001089_TD05** **MCF001089_TD06** |
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139 =============== ================== ================== ================== ================== ================== ================== |
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140 2_3-PG 0.9711 0.968 0.9909 0.991 0.40 0.9 |
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141 2-OHGLu 0.01719 0.0246 0.554 0.555 0.73 0.68 |
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142 Glc6P 0.06 0.66 2683 0.06 2068 2172 |
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143 Gly3P 0.06 0.06 0.06 1 5 3 |
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144 IsoCit 0.06 1 0.49 0.36 6 10 |
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145 =============== ================== ================== ================== ================== ================== ================== |
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146 |
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147 |
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148 **Metadata File Information** |
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149 |
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150 Provide a tab-separated file that has the names of the samples in the first column and one header row. |
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151 Column names must be exactly in this order: |
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152 |
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153 name_to_plot |
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154 condition |
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155 timepoint |
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156 timenum |
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157 compartment |
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158 original_name |
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159 |
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160 |
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161 Example **Metadata File**: |
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162 |
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163 |
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164 ==================== =============== ============= ============ ================ ================= |
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165 **name_to_plot** **condition** **timepoint** **timenum** **compartment** **original_name** |
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166 -------------------- --------------- ------------- ------------ ---------------- ----------------- |
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167 Control_cell_T0-1 Control T0 0 cell MCF001089_TD01 |
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168 Control_cell_T0-2 Control T0 0 cell MCF001089_TD02 |
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169 Control_cell_T0-3 Control T0 0 cell MCF001089_TD03 |
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170 Tumoral_cell_T0-1 Tumoral T0 0 cell MCF001089_TD04 |
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171 Tumoral_cell_T0-2 Tumoral T0 0 cell MCF001089_TD05 |
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172 Tumoral_cell_T0-3 Tumoral T0 0 cell MCF001089_TD06 |
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173 Tumoral_cell_T24-1 Tumoral T24 24 cell MCF001089_TD07 |
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174 Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08 |
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175 Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01 |
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176 Control_med_T24-1 Control T24 24 med MCF001090_TD02 |
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177 Control_med_T24-2 Control T24 24 med MCF001090_TD03 |
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178 Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04 |
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179 Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05 |
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180 Control_med_T0-1 Control T0 0 med MCF001090_TD06 |
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181 Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07 |
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182 Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08 |
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183 ==================== =============== ============= ============ ================ ================= |
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184 |
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185 |
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186 The column **original_name** must have the names of the samples as given in your data. |
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187 |
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188 The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that |
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189 are meaningful is a better choice, as we will take them to display the results. |
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190 |
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191 The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc) |
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192 nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!). |
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193 |
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194 The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results' files names: the longer the |
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195 compartments names are, the longer the output files' names! Please pick short and clear abbreviations to fill this column. |
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196 |
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197 |
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198 **Running the analysis** |
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199 |
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200 You can precise how you want your analysis to be executed, there exist hints on use that will guide you, next to the parameters. |
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201 |
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202 Our tool automatically analyzes the integrality of your data (one global PCA analysis), and also splits your data by timepoint to generate PCA results by timepoint (which is convenient to explore the "grouping" of conditions), but if you only have one condition you can discard them. |
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203 |
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204 The output consists of two .csv files for each performed PCA analysis (one file with the Principal Components (PC), one file with the variances). |
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205 |
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206 **Available data for testing** |
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207 |
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208 You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent |
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209 files for you are located in the subfolders inside the data folder). |
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210 You can also use the minimal data examples from https://zenodo.org/record/8380706 |
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211 |
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212 ]]> |
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213 </help> |
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214 <expand macro="citations" /> |
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215 </tool> |