Mercurial > repos > iuc > tracegroomer

annotate macros.xml @ 1:c6a7bbc6066d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
author iuc
date Tue, 03 Sep 2024 19:22:57 +0000
parents 5f7d672647b0
children
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5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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1 <macros>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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2 <token name="@TOOL_VERSION@">0.1.4</token>
1
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
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3 <token name="@VERSION_SUFFIX@">1</token>
0
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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4 <xml name="requirements">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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5 <requirements>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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6 <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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7 </requirements>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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8 </xml>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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9 <xml name="input_datasets">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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10 <param name="labeled_metabo_file" type="data" optional="false" format="tabular,xlsx" label="Labeled metabolomics file"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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11 <param name="sample_metadata_path" type="data" format="tabular" label="sample metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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12 <param name="amount_material" type="data" optional="true" format="interval" label="amount material" help="Absolute path to the file having the amount of material by sample, for the normalization. This file must be a tab delimited file with exactly 2 columns with a header: the first column contains the original names of the samples, and the second column the numbers (tissue weight, number of cells, volume, etc)"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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13 <param name="remove_these_metabolites" type="data" optional="true" format="interval" label="remove metabolites using this file" help="Absolute path to the tab delimited file with columns: compartment, metabolite. This file lists the metabolites to be completely excluded, compartment specific. Defining such exclusion list requires deep knowledge of the data by the user (measurements coherence/quality, etc)"/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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14 <conditional name="type_of_file">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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15 <param name="type_of_file_selector" type="select" label="Choose which type of input file is used" help="One of the following: IsoCor_out_tsv|rule_tsv|VIBMEC_xlsx|generic_xlsx">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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16 <option value="IsoCor_out_tsv" selected="true">isocor output file</option>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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17 <option value="VIBMEC_xlsx">VIBMEC xlsx file</option>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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18 <option value="generic_xlsx">generic xlsx file</option>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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19 <option value="rule_tsv">rule tsv file</option>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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20 </param>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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21 <when value="IsoCor_out_tsv">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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22 </when>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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23 <when value="generic_xlsx">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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24 <param name="sheetname" type="text" value="isotopologuesCorrValues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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25 <sanitizer invalid_char="">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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26 <valid initial="string.ascii_letters,string.digits">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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27 <add value="_" />
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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28 </valid>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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29 </sanitizer>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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30 </param>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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31 </when>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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32 <when value="VIBMEC_xlsx">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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33 <param name="raw_abundance_sheet_name" type="text" value="rawAbundances" optional="false" label="name of the sheet containing the raw abundances values" >
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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34 <sanitizer invalid_char="">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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35 <valid initial="string.ascii_letters,string.digits">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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36 <add value="_" />
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37 </valid>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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38 </sanitizer>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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39 </param>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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40 <param name="frac_contribution_sheet_name" type="text" value="FracContribution_C" optional="false" label="name of the sheet containing the mean enrichment values" >
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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41 <sanitizer invalid_char="">
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42 <valid initial="string.ascii_letters,string.digits">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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43 <add value="_" />
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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44 </valid>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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45 </sanitizer>
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46 </param>
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47 <param name="corrected_isotopologues_sheet_name" type="text" value="CorrectedIsotopologues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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48 <sanitizer invalid_char="">
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49 <valid initial="string.ascii_letters,string.digits">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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50 <add value="_" />
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51 </valid>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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52 </sanitizer>
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53 </param>
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54 </when>
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55 <when value="rule_tsv">
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56 <param name="variable_metadata_path" type="data" format="tabular" label="variable metadata file" help="The metadata, a unique file with the description of the samples in your measures files. This is compulsory, see section Metadata File Information."/>
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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57 <section name="columns_variable_metadata_description" title="variable metadata file columns description" expanded="false">
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58 <param name="identifier" type="text" value="ID" optional="false" label="identifier of your metabolite in variable metadata file" >
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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59 <sanitizer invalid_char="">
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60 <valid initial="string.ascii_letters,string.digits">
5f7d672647b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
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61 <add value="_" />
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62 </valid>
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63 </sanitizer>
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64 </param>
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65 <param name="compound" type="text" value="metabolite_name" optional="false" label="name of your metabolite in variable metadata file (formula is also accepted)" >
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66 <sanitizer invalid_char="">
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67 <valid initial="string.ascii_letters,string.digits">
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68 <add value="_" />
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69 </valid>
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70 </sanitizer>
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71 </param>
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72 <param name="isotopologue_number" value="isotope_numeric" type="text" optional="false" label="isotopologue number in variable metadata file" >
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73 <sanitizer invalid_char="">
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74 <valid initial="string.ascii_letters,string.digits">
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75 <add value="_" />
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76 </valid>
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77 </sanitizer>
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78 </param>
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79 </section>
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80 </when>
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81 </conditional>
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82 </xml>
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83 <xml name="advanced_options">
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84 <section name="advanced_options" title="Advanced options" expanded="false" help="Default values explained in our Wiki page (link at the end of the Help section)">
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85 <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" checked="true" falsevalue="--no-div_isotopologues_by_amount_material" label="isotopologues division by amount material" help="Apply normalization by the amount of material at the level of isotopologue absolute values. Immediately after this, and before any other computation, tracegroomer re-computes all derived (thus normalized) metrics"/>
c6a7bbc6066d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 26f0c7344995bfa302db821e77ae717636a4f4b2
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86 <param name="alternative_div_amount_material" type="boolean" truevalue="--alternative_div_amount_material" checked="true" falsevalue="--no-alternative_div_amount_material" label="alternative division of values by amount material" help="In the normalisation by the amount of material, not only the division of the given absolute values by these amounts is performed, but also the product of the resulting quotients 'q' and the averaged amount of material 'a' (q x a) so abundance units are preserved"/>
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87 <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" checked="false" falsevalue="--no-isotopologues_preview" label="Plot isotopologues" help="Generate simple plots that give a general overview of the isotopologue proportions given by the user. Performs a scatter plot of the individual isotopologue proportions for all metabolites, as well as a plot of the sums of isotopologue proportions (the sum must be equal to 1 for each metabolite and sample)"/>
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88 <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" checked="true" falsevalue="--no-fractions_stomp_values" label="Stomp fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
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89 <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" checked="true" falsevalue="--no-subtract_blankavg" label="Subtract blanks avg (VIB input only)" help="from samples' abundances, subtracts the average of the blanks for all metabolites across all samples. Note that the Internal Standards are not subjected to this operation, as recommended by VIB platform"/>
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90 <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" checked="true" falsevalue="--no-under_detection_limit_set_nan" label="Limit Of Detection (VIB input only)" help="The Limit Of Detection, LOD, corresponds to the averaged blanks abundance values, multiplied by three times the blanks standard deviation. By default, any value that is strictly inferior to its corresponding LOD, is converted into NaN"/>
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91 <param name="use_internal_standard" type="text" optional="true" help="The name of the internal standard, which is a compound or metabolite that has been stated as reference signal. By providing this name, the normalization by the internal standard is automatically performed" label="internal standard" />
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92 <param name="isosprop_min_admitted" type="float" min="-1.0" max="1.0" value="-0.5" label="isotopologues cutoff" help="Metabolites whose isotopologue proportions are less or equal to this cutoff, are removed"/>
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93 <param name="output_files_extension" type="select" value="tsv" display="radio" label="output files extension" help="Note that tab delimited files are always produced, for any chosen extension">
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94 <option value="tsv">tsv</option>
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95 <option value="csv">csv</option>
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96 </param>
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97 </section>
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98 </xml>
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99 <xml name="citations">
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100 <citations>
1
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101 <citation type="doi">10.1093/bioinformatics/btae282</citation>
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102 <citation type="bibtex">
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103 @software{Galvis_Rodriguez_DIMet,
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104 author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},
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105 license = {MIT},
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106 title = {{DIMet}},
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107 url = {https://github.com/cbib/DIMet}
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108 }
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109 </citation>
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110 </citations>
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111
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112 </xml>
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113 </macros>