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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:36:05 +0000
parents f072d901c63c
children
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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:
5
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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 composition ancom" id="qiime2__composition__ancom" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Apply ANCOM to identify features that differ in abundance.</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 composition</version_command>
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22 <command detect_errors="exit_code">q2galaxy run composition ancom '$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="table" type="data" format="qza" label="table: FeatureTable[Composition]" help="[required] The feature table to be used for ANCOM computation.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Composition]"/>
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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 ['FeatureTable[Composition]']</validator>
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32 </param>
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33 <conditional name="metadata">
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34 <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] The categorical sample metadata column to test for differential abundance across.">
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35 <option value="tsv" selected="true">Metadata from TSV</option>
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36 <option value="qza">Metadata from Artifact</option>
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37 </param>
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38 <when value="tsv">
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39 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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40 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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41 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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42 </param>
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43 </when>
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44 <when value="qza">
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45 <param name="source" type="data" format="qza" label="Metadata Source"/>
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46 <param name="column" type="text" label="Column Name">
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47 <validator type="empty_field"/>
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48 </param>
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49 </when>
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50 </conditional>
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51 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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52 <param name="transform_function" type="select" label="transform_function: Str % Choices('sqrt', 'log', 'clr')" display="radio">
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53 <option value="sqrt">sqrt</option>
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54 <option value="log">log</option>
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55 <option value="clr" selected="true">clr</option>
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56 </param>
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57 <param name="difference_function" type="select" label="difference_function: Str % Choices('mean_difference', 'f_statistic')" display="radio">
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58 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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59 <option value="mean_difference">mean_difference</option>
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60 <option value="f_statistic">f_statistic</option>
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61 </param>
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62 <param name="filter_missing" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="filter_missing: Bool" help="[default: No] If True, samples with missing metadata values will be filtered from the table prior to analysis. If False, an error will be raised if there are any missing metadata values."/>
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63 </section>
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64 </inputs>
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65 <outputs>
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66 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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67 </outputs>
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68 <tests/>
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69 <help>
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70 QIIME 2: composition ancom
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71 ==========================
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72 Apply ANCOM to identify features that differ in abundance.
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73
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74
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75 Outputs:
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76 --------
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77 :visualization.qzv: &lt;no description&gt;
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78
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81 Description:
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82 ------------
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83 Apply Analysis of Composition of Microbiomes (ANCOM) to identify features that are differentially abundant across groups.
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86 |
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88 </help>
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89 <citations>
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90 <citation type="doi">10.3402/mehd.v26.27663</citation>
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91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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92 </citations>
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93 </tool>