Mercurial > repos > q2d2 > qiime2__sample_classifier__heatmap
annotate qiime2__sample_classifier__heatmap.xml @ 5:e2c3a69905fe draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
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| date | Wed, 30 Oct 2024 19:56:27 +0000 |
| parents | 8fa6957e6cb0 |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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d15d1e895aed
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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3 Copyright (c) 2024, QIIME 2 development team. |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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9 q2galaxy (version: 2024.10.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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11 qiime2 (version: 2024.10.1) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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13 <tool name="qiime2 sample-classifier heatmap" id="qiime2__sample_classifier__heatmap" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Generate heatmap of important features.</description> |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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15 <xrefs> |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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16 <xref type="bio.tools">qiime2</xref> |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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17 </xrefs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <requirements> |
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e2c3a69905fe
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 </requirements> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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21 <version_command>q2galaxy version sample_classifier</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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22 <command detect_errors="exit_code">q2galaxy run sample_classifier heatmap '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 </configfiles> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <inputs> |
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d15d1e895aed
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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27 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence | Composition]" help="[required] Feature table containing all features that should be used for target prediction."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 5f71b597c9495eae67a447744fded834f56ca1f7
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29 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
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30 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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8fa6957e6cb0
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit c7e80dcda727ce63b42aa8a946e9330310929797
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31 <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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32 <filter type="add_value" value="FeatureTable[Composition]"/> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 </param> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 <param name="importance" type="data" format="qza" label="importance: FeatureData[Importance]" help="[required] Feature importances."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <options options_filter_attribute="metadata.semantic_type"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <filter type="add_value" value="FeatureData[Importance]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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40 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Importance]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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41 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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42 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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43 <conditional name="sample_metadata"> |
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9d749a1b0f69
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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44 <param name="type" type="select" label="sample_metadata: MetadataColumn[Categorical]" help="[optional] Sample metadata column to use for sample labeling or grouping."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 <option value="none" selected="true">None (default)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 <option value="tsv">Metadata from TSV</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 <option value="qza">Metadata from Artifact</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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48 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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49 <when value="none"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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50 <when value="tsv"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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51 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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52 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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53 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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54 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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55 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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56 <when value="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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57 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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58 <param name="column" type="text" label="Column Name"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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59 <validator type="empty_field"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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60 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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61 </when> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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62 </conditional> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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63 <conditional name="feature_metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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64 <param name="type" type="select" label="feature_metadata: MetadataColumn[Categorical]" help="[optional] Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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65 <option value="none" selected="true">None (default)</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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66 <option value="tsv">Metadata from TSV</option> |
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67 <option value="qza">Metadata from Artifact</option> |
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68 </param> |
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69 <when value="none"/> |
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70 <when value="tsv"> |
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71 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> |
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72 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> |
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73 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> |
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74 </param> |
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75 </when> |
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76 <when value="qza"> |
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77 <param name="source" type="data" format="qza" label="Metadata Source"/> |
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78 <param name="column" type="text" label="Column Name"> |
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79 <validator type="empty_field"/> |
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80 </param> |
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81 </when> |
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82 </conditional> |
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83 <param name="feature_count" type="integer" min="0" value="50" label="feature_count: Int % Range(0, None)" help="[default: 50] Filter feature table to include top N most important features. Set to zero to include all features."/> |
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84 <param name="importance_threshold" type="float" min="0" value="0" label="importance_threshold: Float % Range(0, None)" help="[default: 0] Filter feature table to exclude any features with an importance score less than this threshold. Set to zero to include all features."/> |
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85 <param name="group_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="group_samples: Bool" help="[default: No] Group samples by sample metadata."/> |
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86 <param name="normalize" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="normalize: Bool" help="[default: Yes] Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table."/> |
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87 <param name="missing_samples" type="select" label="missing_samples: Str % Choices('error', 'ignore')" display="radio"> |
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88 <option value="error">error</option> |
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89 <option value="ignore" selected="true">ignore</option> |
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90 </param> |
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91 <param name="metric" type="select" label="metric: Str % Choices('braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')"> |
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92 <option value="braycurtis" selected="true">braycurtis</option> |
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93 <option value="canberra">canberra</option> |
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94 <option value="chebyshev">chebyshev</option> |
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95 <option value="cityblock">cityblock</option> |
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96 <option value="correlation">correlation</option> |
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97 <option value="cosine">cosine</option> |
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98 <option value="dice">dice</option> |
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99 <option value="euclidean">euclidean</option> |
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100 <option value="hamming">hamming</option> |
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101 <option value="jaccard">jaccard</option> |
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102 <option value="kulsinski">kulsinski</option> |
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103 <option value="mahalanobis">mahalanobis</option> |
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104 <option value="matching">matching</option> |
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105 <option value="minkowski">minkowski</option> |
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106 <option value="rogerstanimoto">rogerstanimoto</option> |
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107 <option value="russellrao">russellrao</option> |
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108 <option value="seuclidean">seuclidean</option> |
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109 <option value="sokalmichener">sokalmichener</option> |
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110 <option value="sokalsneath">sokalsneath</option> |
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111 <option value="sqeuclidean">sqeuclidean</option> |
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112 <option value="yule">yule</option> |
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113 </param> |
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114 <param name="method" type="select" label="method: Str % Choices('average', 'centroid', 'complete', 'median', 'single', 'ward', 'weighted')"> |
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115 <option value="average" selected="true">average</option> |
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116 <option value="centroid">centroid</option> |
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117 <option value="complete">complete</option> |
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118 <option value="median">median</option> |
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119 <option value="single">single</option> |
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120 <option value="ward">ward</option> |
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121 <option value="weighted">weighted</option> |
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122 </param> |
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123 <param name="cluster" type="select" label="cluster: Str % Choices('both', 'features', 'none', 'samples')" display="radio"> |
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124 <option value="both">both</option> |
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125 <option value="features" selected="true">features</option> |
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126 <option value="none">none</option> |
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127 <option value="samples">samples</option> |
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128 </param> |
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129 <param name="color_scheme" type="select" label="color_scheme: Str % Choices('Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Vega10', 'Vega10_r', 'Vega20', 'Vega20_r', 'Vega20b', 'Vega20b_r', 'Vega20c', 'Vega20c_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'icefire', 'icefire_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'mako', 'mako_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'rocket', 'rocket_r', 'seismic', 'seismic_r', 'spectral', 'spectral_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'viridis', 'viridis_r', 'vlag', 'vlag_r', 'winter', 'winter_r')"> |
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130 <option value="Accent">Accent</option> |
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131 <option value="Accent_r">Accent_r</option> |
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132 <option value="Blues">Blues</option> |
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133 <option value="Blues_r">Blues_r</option> |
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134 <option value="BrBG">BrBG</option> |
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135 <option value="BrBG_r">BrBG_r</option> |
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136 <option value="BuGn">BuGn</option> |
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137 <option value="BuGn_r">BuGn_r</option> |
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138 <option value="BuPu">BuPu</option> |
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139 <option value="BuPu_r">BuPu_r</option> |
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140 <option value="CMRmap">CMRmap</option> |
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141 <option value="CMRmap_r">CMRmap_r</option> |
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142 <option value="Dark2">Dark2</option> |
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143 <option value="Dark2_r">Dark2_r</option> |
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144 <option value="GnBu">GnBu</option> |
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145 <option value="GnBu_r">GnBu_r</option> |
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146 <option value="Greens">Greens</option> |
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147 <option value="Greens_r">Greens_r</option> |
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148 <option value="Greys">Greys</option> |
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149 <option value="Greys_r">Greys_r</option> |
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150 <option value="OrRd">OrRd</option> |
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151 <option value="OrRd_r">OrRd_r</option> |
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152 <option value="Oranges">Oranges</option> |
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153 <option value="Oranges_r">Oranges_r</option> |
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154 <option value="PRGn">PRGn</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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155 <option value="PRGn_r">PRGn_r</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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156 <option value="Paired">Paired</option> |
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157 <option value="Paired_r">Paired_r</option> |
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158 <option value="Pastel1">Pastel1</option> |
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159 <option value="Pastel1_r">Pastel1_r</option> |
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160 <option value="Pastel2">Pastel2</option> |
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161 <option value="Pastel2_r">Pastel2_r</option> |
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162 <option value="PiYG">PiYG</option> |
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163 <option value="PiYG_r">PiYG_r</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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164 <option value="PuBu">PuBu</option> |
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165 <option value="PuBuGn">PuBuGn</option> |
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166 <option value="PuBuGn_r">PuBuGn_r</option> |
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167 <option value="PuBu_r">PuBu_r</option> |
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168 <option value="PuOr">PuOr</option> |
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169 <option value="PuOr_r">PuOr_r</option> |
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170 <option value="PuRd">PuRd</option> |
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171 <option value="PuRd_r">PuRd_r</option> |
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172 <option value="Purples">Purples</option> |
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173 <option value="Purples_r">Purples_r</option> |
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174 <option value="RdBu">RdBu</option> |
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175 <option value="RdBu_r">RdBu_r</option> |
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176 <option value="RdGy">RdGy</option> |
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177 <option value="RdGy_r">RdGy_r</option> |
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178 <option value="RdPu">RdPu</option> |
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179 <option value="RdPu_r">RdPu_r</option> |
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180 <option value="RdYlBu">RdYlBu</option> |
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181 <option value="RdYlBu_r">RdYlBu_r</option> |
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182 <option value="RdYlGn">RdYlGn</option> |
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183 <option value="RdYlGn_r">RdYlGn_r</option> |
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184 <option value="Reds">Reds</option> |
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185 <option value="Reds_r">Reds_r</option> |
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186 <option value="Set1">Set1</option> |
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187 <option value="Set1_r">Set1_r</option> |
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188 <option value="Set2">Set2</option> |
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189 <option value="Set2_r">Set2_r</option> |
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190 <option value="Set3">Set3</option> |
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191 <option value="Set3_r">Set3_r</option> |
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192 <option value="Spectral">Spectral</option> |
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193 <option value="Spectral_r">Spectral_r</option> |
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194 <option value="Vega10">Vega10</option> |
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195 <option value="Vega10_r">Vega10_r</option> |
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196 <option value="Vega20">Vega20</option> |
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197 <option value="Vega20_r">Vega20_r</option> |
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198 <option value="Vega20b">Vega20b</option> |
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199 <option value="Vega20b_r">Vega20b_r</option> |
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200 <option value="Vega20c">Vega20c</option> |
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201 <option value="Vega20c_r">Vega20c_r</option> |
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202 <option value="Wistia">Wistia</option> |
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203 <option value="Wistia_r">Wistia_r</option> |
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204 <option value="YlGn">YlGn</option> |
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205 <option value="YlGnBu">YlGnBu</option> |
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206 <option value="YlGnBu_r">YlGnBu_r</option> |
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207 <option value="YlGn_r">YlGn_r</option> |
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208 <option value="YlOrBr">YlOrBr</option> |
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209 <option value="YlOrBr_r">YlOrBr_r</option> |
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210 <option value="YlOrRd">YlOrRd</option> |
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211 <option value="YlOrRd_r">YlOrRd_r</option> |
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212 <option value="afmhot">afmhot</option> |
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213 <option value="afmhot_r">afmhot_r</option> |
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214 <option value="autumn">autumn</option> |
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215 <option value="autumn_r">autumn_r</option> |
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216 <option value="binary">binary</option> |
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217 <option value="binary_r">binary_r</option> |
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218 <option value="bone">bone</option> |
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219 <option value="bone_r">bone_r</option> |
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220 <option value="brg">brg</option> |
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221 <option value="brg_r">brg_r</option> |
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222 <option value="bwr">bwr</option> |
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223 <option value="bwr_r">bwr_r</option> |
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224 <option value="cividis">cividis</option> |
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225 <option value="cividis_r">cividis_r</option> |
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226 <option value="cool">cool</option> |
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227 <option value="cool_r">cool_r</option> |
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228 <option value="coolwarm">coolwarm</option> |
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229 <option value="coolwarm_r">coolwarm_r</option> |
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230 <option value="copper">copper</option> |
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231 <option value="copper_r">copper_r</option> |
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232 <option value="cubehelix">cubehelix</option> |
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233 <option value="cubehelix_r">cubehelix_r</option> |
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234 <option value="flag">flag</option> |
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235 <option value="flag_r">flag_r</option> |
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236 <option value="gist_earth">gist_earth</option> |
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237 <option value="gist_earth_r">gist_earth_r</option> |
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238 <option value="gist_gray">gist_gray</option> |
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239 <option value="gist_gray_r">gist_gray_r</option> |
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240 <option value="gist_heat">gist_heat</option> |
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241 <option value="gist_heat_r">gist_heat_r</option> |
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242 <option value="gist_ncar">gist_ncar</option> |
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243 <option value="gist_ncar_r">gist_ncar_r</option> |
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244 <option value="gist_rainbow">gist_rainbow</option> |
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245 <option value="gist_rainbow_r">gist_rainbow_r</option> |
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246 <option value="gist_stern">gist_stern</option> |
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247 <option value="gist_stern_r">gist_stern_r</option> |
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248 <option value="gist_yarg">gist_yarg</option> |
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249 <option value="gist_yarg_r">gist_yarg_r</option> |
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250 <option value="gnuplot">gnuplot</option> |
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251 <option value="gnuplot2">gnuplot2</option> |
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252 <option value="gnuplot2_r">gnuplot2_r</option> |
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253 <option value="gnuplot_r">gnuplot_r</option> |
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254 <option value="gray">gray</option> |
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255 <option value="gray_r">gray_r</option> |
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256 <option value="hot">hot</option> |
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257 <option value="hot_r">hot_r</option> |
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258 <option value="hsv">hsv</option> |
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259 <option value="hsv_r">hsv_r</option> |
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260 <option value="icefire">icefire</option> |
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261 <option value="icefire_r">icefire_r</option> |
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262 <option value="inferno">inferno</option> |
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263 <option value="inferno_r">inferno_r</option> |
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264 <option value="jet">jet</option> |
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265 <option value="jet_r">jet_r</option> |
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266 <option value="magma">magma</option> |
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267 <option value="magma_r">magma_r</option> |
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268 <option value="mako">mako</option> |
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269 <option value="mako_r">mako_r</option> |
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270 <option value="nipy_spectral">nipy_spectral</option> |
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271 <option value="nipy_spectral_r">nipy_spectral_r</option> |
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272 <option value="ocean">ocean</option> |
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273 <option value="ocean_r">ocean_r</option> |
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274 <option value="pink">pink</option> |
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275 <option value="pink_r">pink_r</option> |
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276 <option value="plasma">plasma</option> |
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277 <option value="plasma_r">plasma_r</option> |
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278 <option value="prism">prism</option> |
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279 <option value="prism_r">prism_r</option> |
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280 <option value="rainbow">rainbow</option> |
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281 <option value="rainbow_r">rainbow_r</option> |
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282 <option value="rocket" selected="true">rocket</option> |
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283 <option value="rocket_r">rocket_r</option> |
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284 <option value="seismic">seismic</option> |
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285 <option value="seismic_r">seismic_r</option> |
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286 <option value="spectral">spectral</option> |
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287 <option value="spectral_r">spectral_r</option> |
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288 <option value="spring">spring</option> |
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289 <option value="spring_r">spring_r</option> |
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290 <option value="summer">summer</option> |
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291 <option value="summer_r">summer_r</option> |
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292 <option value="tab10">tab10</option> |
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293 <option value="tab10_r">tab10_r</option> |
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294 <option value="tab20">tab20</option> |
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295 <option value="tab20_r">tab20_r</option> |
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296 <option value="tab20b">tab20b</option> |
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297 <option value="tab20b_r">tab20b_r</option> |
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298 <option value="tab20c">tab20c</option> |
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299 <option value="tab20c_r">tab20c_r</option> |
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300 <option value="terrain">terrain</option> |
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301 <option value="terrain_r">terrain_r</option> |
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302 <option value="viridis">viridis</option> |
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303 <option value="viridis_r">viridis_r</option> |
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304 <option value="vlag">vlag</option> |
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305 <option value="vlag_r">vlag_r</option> |
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306 <option value="winter">winter</option> |
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307 <option value="winter_r">winter_r</option> |
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308 </param> |
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309 </section> |
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310 </inputs> |
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311 <outputs> |
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312 <data name="heatmap" format="qzv" label="${tool.name} on ${on_string}: heatmap.qzv" from_work_dir="heatmap.qzv"/> |
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313 <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> |
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314 </outputs> |
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315 <tests/> |
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316 <help> |
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317 QIIME 2: sample-classifier heatmap |
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318 ================================== |
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319 Generate heatmap of important features. |
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320 |
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321 |
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322 Outputs: |
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323 -------- |
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324 :heatmap.qzv: Heatmap of important features. |
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325 :filtered_table.qza: Filtered feature table containing data displayed in heatmap. |
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326 |
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327 | |
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328 |
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329 Description: |
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330 ------------ |
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331 Generate a heatmap of important features. Features are filtered based on importance scores; samples are optionally grouped by sample metadata; and a heatmap is generated that displays (normalized) feature abundances per sample. |
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332 |
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333 |
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334 | |
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335 |
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336 </help> |
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337 <citations> |
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338 <citation type="doi">10.21105/joss.00934</citation> |
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339 <citation type="bibtex">@article{cite2, |
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340 author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard}, |
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341 journal = {Journal of machine learning research}, |
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342 number = {Oct}, |
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343 pages = {2825--2830}, |
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344 title = {Scikit-learn: Machine learning in Python}, |
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345 volume = {12}, |
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346 year = {2011} |
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347 } |
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348 </citation> |
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349 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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350 </citations> |
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351 </tool> |