Mercurial > repos > q2d2 > qiime2__diversity_lib__weighted_unifrac
annotate qiime2__diversity_lib__weighted_unifrac.xml @ 4:eafeb0b89ece draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:21:59 +0000 |
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e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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5f6f3053916b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 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__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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eafeb0b89ece
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
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9 q2galaxy (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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10 for: |
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eafeb0b89ece
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
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11 qiime2 (version: 2024.5.0) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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eafeb0b89ece
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 diversity-lib weighted-unifrac" id="qiime2__diversity_lib__weighted_unifrac" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Weighted Unifrac</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit c7e80dcda727ce63b42aa8a946e9330310929797
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version diversity_lib</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run diversity_lib weighted_unifrac '$inputs'</command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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20 <configfiles> |
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5f6f3053916b
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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21 <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__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Weighted Unifrac should be computed."> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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85f762ce919f
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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26 <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__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <filter type="add_value" value="FeatureTable[Frequency]"/> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 </options> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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30 </param> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <param name="phylogeny" type="data" format="qza" label="phylogeny: Phylogeny[Rooted]" help="[required] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree."> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <options options_filter_attribute="metadata.semantic_type"> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <filter type="add_value" value="Phylogeny[Rooted]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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34 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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35 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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36 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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38 <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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39 </section> |
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40 </inputs> |
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41 <outputs> |
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42 <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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43 </outputs> |
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44 <tests> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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45 <test> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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46 <param name="table" value="weighted_unifrac.test0.feature-table.qza" ftype="qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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47 <param name="phylogeny" value="weighted_unifrac.test0.phylogeny.qza" ftype="qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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48 <output name="distance_matrix" ftype="qza"> |
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49 <assert_contents> |
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50 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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51 <has_line_matching expression="type: DistanceMatrix"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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52 </has_archive_member> |
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53 </assert_contents> |
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54 </output> |
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55 </test> |
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56 <test> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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57 <param name="table" value="weighted_unifrac.test1.feature-table.qza" ftype="qza"/> |
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58 <param name="phylogeny" value="weighted_unifrac.test1.phylogeny.qza" ftype="qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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59 <output name="distance_matrix" ftype="qza"> |
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60 <assert_contents> |
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61 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
e2279c0e696c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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62 <has_line_matching expression="type: DistanceMatrix"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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63 </has_archive_member> |
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64 </assert_contents> |
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65 </output> |
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66 </test> |
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67 <test> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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68 <param name="table" value="weighted_unifrac.test2.feature-table.qza" ftype="qza"/> |
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69 <param name="phylogeny" value="weighted_unifrac.test2.phylogeny.qza" ftype="qza"/> |
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70 <output name="distance_matrix" ftype="qza"> |
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71 <assert_contents> |
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72 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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73 <has_line_matching expression="type: DistanceMatrix"/> |
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74 </has_archive_member> |
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75 </assert_contents> |
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76 </output> |
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77 </test> |
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78 <test> |
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79 <param name="table" value="weighted_unifrac.test3.feature-table.qza" ftype="qza"/> |
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80 <param name="phylogeny" value="weighted_unifrac.test3.phylogeny.qza" ftype="qza"/> |
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81 <param name="bypass_tips" value="__q2galaxy__::literal::True"/> |
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82 <output name="distance_matrix" ftype="qza"> |
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83 <assert_contents> |
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84 <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> |
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85 <has_line_matching expression="type: DistanceMatrix"/> |
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86 </has_archive_member> |
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87 </assert_contents> |
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88 </output> |
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89 </test> |
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90 </tests> |
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91 <help> |
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92 QIIME 2: diversity-lib weighted-unifrac |
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93 ======================================= |
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94 Weighted Unifrac |
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95 |
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96 |
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97 Outputs: |
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98 -------- |
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99 :distance_matrix.qza: Distance matrix for Unweighted Unifrac. |
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100 |
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101 | |
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102 |
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103 Description: |
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104 ------------ |
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105 Compute Weighted Unifrac for each sample in a feature table |
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106 |
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107 Examples: |
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108 --------- |
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109 |
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110 run on one core (by default) |
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111 **************************** |
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112 Using the ``qiime2 diversity-lib weighted-unifrac`` tool: |
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113 #. Set *"table"* to ``#: feature-table.qza`` |
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114 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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115 #. Press the ``Execute`` button. |
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116 |
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117 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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118 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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119 |
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120 .. list-table:: |
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121 :align: left |
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122 :header-rows: 1 |
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123 |
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124 * - History Name |
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125 - *"Name"* to set (be sure to press ``Save``) |
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126 * - ``#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`` |
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127 - ``weighted-unifrac-dm.qza`` |
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128 |
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129 to run on n cores, replace 1 here with your preferred integer |
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130 ************************************************************* |
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131 Using the ``qiime2 diversity-lib weighted-unifrac`` tool: |
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132 #. Set *"table"* to ``#: feature-table.qza`` |
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133 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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134 #. Press the ``Execute`` button. |
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135 |
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136 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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137 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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138 |
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139 .. list-table:: |
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140 :align: left |
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141 :header-rows: 1 |
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142 |
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143 * - History Name |
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144 - *"Name"* to set (be sure to press ``Save``) |
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145 * - ``#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`` |
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146 - ``weighted-unifrac-dm.qza`` |
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147 |
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148 use 'auto' to run on all of host system's available CPU cores |
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149 ************************************************************* |
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150 Using the ``qiime2 diversity-lib weighted-unifrac`` tool: |
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151 #. Set *"table"* to ``#: feature-table.qza`` |
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152 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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153 #. Press the ``Execute`` button. |
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154 |
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155 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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156 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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157 |
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158 .. list-table:: |
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159 :align: left |
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160 :header-rows: 1 |
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161 |
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162 * - History Name |
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163 - *"Name"* to set (be sure to press ``Save``) |
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164 * - ``#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`` |
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165 - ``weighted-unifrac-dm.qza`` |
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166 |
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167 use bypass_tips to trade specificity for reduced compute time |
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168 ************************************************************* |
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169 | bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time. |
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170 Using the ``qiime2 diversity-lib weighted-unifrac`` tool: |
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171 #. Set *"table"* to ``#: feature-table.qza`` |
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172 #. Set *"phylogeny"* to ``#: phylogeny.qza`` |
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173 #. Expand the ``additional options`` section |
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174 |
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175 - Set *"bypass_tips"* to ``Yes`` |
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176 |
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177 #. Press the ``Execute`` button. |
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178 |
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179 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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180 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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181 |
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182 .. list-table:: |
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183 :align: left |
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184 :header-rows: 1 |
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185 |
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186 * - History Name |
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187 - *"Name"* to set (be sure to press ``Save``) |
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188 * - ``#: qiime2 diversity-lib weighted-unifrac [...] : distance_matrix.qza`` |
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189 - ``weighted-unifrac-dm.qza`` |
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190 |
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191 |
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192 | |
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193 |
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194 </help> |
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195 <citations> |
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196 <citation type="doi">10.1128/AEM.71.12.8228-8235.2005</citation> |
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197 <citation type="doi">10.1128/AEM.01996-06</citation> |
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198 <citation type="doi">10.1038/ismej.2009.97</citation> |
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199 <citation type="doi">10.1038/ismej.2010.133</citation> |
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200 <citation type="doi">10.1038/s41592-018-0187-8</citation> |
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201 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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202 </citations> |
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203 </tool> |