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author q2d2
date Wed, 30 Oct 2024 19:38:36 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 diversity procrustes-analysis" id="qiime2__diversity__procrustes_analysis" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Procrustes Analysis</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version diversity</version_command>
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22 <command detect_errors="exit_code">q2galaxy run diversity procrustes_analysis '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="reference" type="data" format="qza" label="reference: PCoAResults" help="[required] The ordination matrix to which data is fitted to.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="PCoAResults"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
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32 </param>
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33 <param name="other" type="data" format="qza" label="other: PCoAResults" help="[required] The ordination matrix that's fitted to the reference ordination.">
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34 <options options_filter_attribute="metadata.semantic_type">
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35 <filter type="add_value" value="PCoAResults"/>
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36 </options>
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37 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator>
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38 </param>
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39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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40 <param name="dimensions" type="integer" min="1" value="5" label="dimensions: Int % Range(1, None)" help="[default: 5] The number of dimensions to use when fitting the two matrices"/>
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41 <conditional name="__q2galaxy__GUI__conditional__permutations__">
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42 <param name="__q2galaxy__GUI__select__" type="select" label="permutations: Int % Range(1, None) | Str % Choices('disable')" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).">
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43 <option value="disable">disable (Str)</option>
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44 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
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45 </param>
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46 <when value="disable">
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47 <param name="permutations" type="hidden" value="disable"/>
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48 </when>
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49 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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50 <param name="permutations" type="integer" min="1" value="999" label="permutations: Int % Range(1, None)" help="[default: 999] The number of permutations to be run when computing p-values. Supplying a value of `disable` will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired)."/>
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51 </when>
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52 </conditional>
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53 </section>
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54 </inputs>
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55 <outputs>
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56 <data name="transformed_reference" format="qza" label="${tool.name} on ${on_string}: transformed_reference.qza" from_work_dir="transformed_reference.qza"/>
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57 <data name="transformed_other" format="qza" label="${tool.name} on ${on_string}: transformed_other.qza" from_work_dir="transformed_other.qza"/>
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58 <data name="disparity_results" format="qza" label="${tool.name} on ${on_string}: disparity_results.qza" from_work_dir="disparity_results.qza"/>
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59 </outputs>
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60 <tests/>
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61 <help>
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62 QIIME 2: diversity procrustes-analysis
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63 ======================================
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64 Procrustes Analysis
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65
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66
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67 Outputs:
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68 --------
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69 :transformed_reference.qza: A normalized version of the "reference" ordination matrix.
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70 :transformed_other.qza: A normalized and fitted version of the "other" ordination matrix.
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71 :disparity_results.qza: The sum of the squares of the pointwise differences between the two input datasets &amp; its p value.
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72
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73 |
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75 Description:
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76 ------------
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77 Fit two ordination matrices with Procrustes analysis
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80 |
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82 </help>
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83 <citations>
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84 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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85 </citations>
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86 </tool>