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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:52:29 +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 feature-table presence-absence" id="qiime2__feature_table__presence_absence" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Convert to presence/absence</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 feature_table</version_command>
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22 <command detect_errors="exit_code">q2galaxy run feature_table presence_absence '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table to be converted into presence/absence abundances.">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureTable[Frequency]"/>
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30 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
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31 </options>
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32 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="presence_absence_table" format="qza" label="${tool.name} on ${on_string}: presence_absence_table.qza" from_work_dir="presence_absence_table.qza"/>
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37 </outputs>
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38 <tests/>
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39 <help>
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40 QIIME 2: feature-table presence-absence
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41 =======================================
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42 Convert to presence/absence
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43
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44
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45 Outputs:
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46 --------
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47 :presence_absence_table.qza: The resulting presence/absence feature table.
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48
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49 |
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51 Description:
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52 ------------
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53 Convert frequencies to binary values indicating presence or absence of a feature in a sample.
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54
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55
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56 |
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57
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58 </help>
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59 <citations>
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60 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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61 </citations>
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62 </tool>