Mercurial > repos > iuc > tracegroomer

annotate macros.xml @ 1:ea6ea4029c47 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 81d7b9e41c36f76a0064a85031156da4a8e72e32
author iuc
date Thu, 22 Aug 2024 18:45:34 +0000
parents 3cb0128a59a6
children 5147f08d67c9
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3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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1 <macros>
1
ea6ea4029c47 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>
0
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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3 <token name="@VERSION_SUFFIX@">0</token>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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4 <xml name="requirements">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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5 <requirements>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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6 <requirement type="package" version="@TOOL_VERSION@">tracegroomer</requirement>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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7 </requirements>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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8 </xml>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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9 <xml name="input_datasets">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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10 <param name="labeled_metabo_file" type="data" optional="false" format="tabular,xlsx" label="Labeled metabolomics file"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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."/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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)"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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)"/>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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14 <conditional name="type_of_file">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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16 <option value="IsoCor_out_tsv" selected="true">isocor output file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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17 <option value="VIBMEC_xlsx">VIBMEC xlsx file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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18 <option value="generic_xlsx">generic xlsx file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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19 <option value="rule_tsv">rule tsv file</option>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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20 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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21 <when value="IsoCor_out_tsv">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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22 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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23 <when value="generic_xlsx">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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24 <param name="sheetname" type="text" value="isotopologuesCorrValues" optional="false" label="name of the sheet containing the isotopologues corrected values" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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25 <sanitizer invalid_char="">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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26 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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27 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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28 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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29 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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30 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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31 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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32 <when value="VIBMEC_xlsx">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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34 <sanitizer invalid_char="">
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35 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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36 <add value="_" />
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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37 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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38 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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39 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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41 <sanitizer invalid_char="">
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42 <valid initial="string.ascii_letters,string.digits">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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43 <add value="_" />
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44 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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45 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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46 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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" >
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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48 <sanitizer invalid_char="">
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49 <valid initial="string.ascii_letters,string.digits">
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50 <add value="_" />
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51 </valid>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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52 </sanitizer>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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53 </param>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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54 </when>
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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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."/>
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57 <section name="columns_variable_metadata_description" title="variable metadata file columns description" expanded="false">
3cb0128a59a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/Tracegroomer commit 6a049d6fe2f2975403086e17f97fab041c311590
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58 <param name="identifier" type="text" value="ID" optional="false" label="identifier of your metabolite in variable metadata file" >
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59 <sanitizer invalid_char="">
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60 <valid initial="string.ascii_letters,string.digits">
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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">
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85
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86 <param name="alternative_div_amount_material" type="boolean" truevalue="--alternative_div_amount_material" falsevalue="" label="alternative isotopologues division 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 and the averaged amount of material is computed"/>
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87 <param name="div_isotopologues_by_amount_material" type="boolean" truevalue="--div_isotopologues_by_amount_material" falsevalue="" label="isotopologues 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"/>
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88 <param name="isotopologues_preview" type="boolean" truevalue="--isotopologues_preview" falsevalue="" label="Plot isotopologue" 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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89 <param name="fractions_stomp_values" type="boolean" truevalue="--fractions_stomp_values" falsevalue="" label="Stomps fractional contributions" help="Stomps fractional contributions (synonym: mean enrichment), and isotopologue proportions, to max 1.0 and min 0.0"/>
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90 <param name="subtract_blankavg" type="boolean" truevalue="--subtract_blankavg" falsevalue="" label="" 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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91 <param name="under_detection_limit_set_nan" type="boolean" truevalue="--under_detection_limit_set_nan" falsevalue="" label="Limit Of Detection" 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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92 <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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93 <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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94 </section>
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95 </xml>
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96 <xml name="citations">
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97 <citations>
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98 <citation type="bibtex">
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99 @software{Galvis_Rodriguez_DIMet,
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100 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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101 license = {MIT},
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102 title = {{DIMet}},
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103 url = {https://github.com/cbib/DIMet}
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104 }
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105 </citation>
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106 </citations>
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107
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108 </xml>
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109 </macros>