Mercurial > repos > q2d2 > qiime2__gneiss__ilr_phylogenetic
annotate qiime2__gneiss__ilr_phylogenetic.xml @ 1:b2f1851509f6 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:56:34 +0000 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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1 <?xml version='1.0' encoding='utf-8'?> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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3 Copyright (c) 2023, QIIME 2 development team. |
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4 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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8 This tool was automatically generated by: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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9 q2galaxy (version: 2022.11.1) |
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10 for: |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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11 qiime2 (version: 2022.11.1) |
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12 --> |
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13 <tool name="qiime2 gneiss ilr-phylogenetic" id="qiime2__gneiss__ilr_phylogenetic" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> |
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14 <description>Isometric Log-ratio Transform applied to a phylogenetic tree</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/core:2022.11</container> |
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17 </requirements> |
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18 <version_command>q2galaxy version gneiss</version_command> |
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19 <command detect_errors="exit_code">q2galaxy run gneiss ilr_phylogenetic '$inputs'</command> |
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20 <configfiles> |
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21 <inputs name="inputs" data_style="paths"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
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23 <inputs> |
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24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | Composition]" help="[required] The feature table containing the samples in which the ilr transform will be performed."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <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__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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27 <filter type="add_value" value="FeatureTable[Composition]"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 </options> |
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]']</validator> |
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30 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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31 <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required] A rooted phylogeny of feature identifiers that defines the partitions of features. Each tip in the hierarchycorresponds 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. This assumes that all of the internal nodes in the tree have labels. This tree may contain polytomic nodes (i.e., nodes with more than two children), in which case they will be bifurcated."> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <options options_filter_attribute="metadata.semantic_type"> |
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33 <filter type="add_value" value="Phylogeny[Rooted]"/> |
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34 </options> |
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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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36 </param> |
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37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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38 <param name="pseudocount" type="float" value="0.5" label="pseudocount: Float" help="[default: 0.5] The value to add to zero counts in the feature table."/> |
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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="balances" format="qza" label="${tool.name} on ${on_string}: balances.qza" from_work_dir="balances.qza"/> |
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43 <data name="hierarchy" format="qza" label="${tool.name} on ${on_string}: hierarchy.qza" from_work_dir="hierarchy.qza"/> |
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44 </outputs> |
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45 <tests/> |
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46 <help> |
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47 QIIME 2: gneiss ilr-phylogenetic |
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48 ================================ |
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49 Isometric Log-ratio Transform applied to a phylogenetic tree |
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50 |
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51 |
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52 Outputs: |
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53 -------- |
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54 :balances.qza: The resulting balances from the ilr transform. |
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55 :hierarchy.qza: Hierarchy from bifurcated phylogeny |
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56 |
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57 | |
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58 |
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59 Description: |
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60 ------------ |
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61 Calculate balances given a rooted phylogeny. |
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62 |
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63 |
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64 | |
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65 |
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66 </help> |
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67 <citations> |
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68 <citation type="bibtex">@article{cite1, |
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69 author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob}, |
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70 journal = {MSystems}, |
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71 number = {1}, |
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72 pages = {e00162--16}, |
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73 publisher = {Am Soc Microbiol}, |
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74 title = {Balance trees reveal microbial niche differentiation}, |
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75 volume = {2}, |
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76 year = {2017} |
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77 } |
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78 </citation> |
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79 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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80 </citations> |
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81 </tool> |