Mercurial > repos > q2d2 > qiime2__feature_table__core_features
annotate qiime2__feature_table__core_features.xml @ 4:5bd93c10087b draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
author | q2d2 |
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date | Mon, 03 Jun 2024 23:24:41 +0000 |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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2 <!-- |
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3 Copyright (c) 2024, 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__feature_table 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__feature_table 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__feature_table 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__feature_table 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__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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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__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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12 --> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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13 <tool name="qiime2 feature-table core-features" id="qiime2__feature_table__core_features" 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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14 <description>Identify core features in table</description> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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15 <requirements> |
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> |
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17 </requirements> |
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18 <version_command>q2galaxy version feature_table</version_command> |
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19 <command detect_errors="exit_code">q2galaxy run feature_table core_features '$inputs'</command> |
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20 <configfiles> |
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/> |
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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]" help="[required] The feature table to use in core features calculations."> |
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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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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26 <filter type="add_value" value="FeatureTable[Frequency]"/> |
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27 </options> |
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> |
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29 </param> |
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
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31 <param name="min_fraction" type="float" min="1e-06" max="0.999999" value="0.5" label="min_fraction: Float % Range(0.0, 1.0, inclusive_start=False)" help="[default: 0.5] The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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32 <param name="max_fraction" type="float" min="0.0" max="1.0" value="1.0" label="max_fraction: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 1.0] The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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33 <param name="steps" type="integer" min="2" value="11" label="steps: Int % Range(2, None)" help="[default: 11] The number of steps to take between `min_fraction` and `max_fraction` for core features calculations. This parameter has no effect if `min_fraction` and `max_fraction` are the same value."/> |
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34 </section> |
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35 </inputs> |
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36 <outputs> |
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37 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> |
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38 </outputs> |
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39 <tests/> |
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40 <help> |
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41 QIIME 2: feature-table core-features |
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42 ==================================== |
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43 Identify core features in table |
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44 |
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45 |
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46 Outputs: |
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47 -------- |
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48 :visualization.qzv: <no description> |
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49 |
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50 | |
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51 |
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52 Description: |
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53 ------------ |
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54 Identify "core" features, which are features observed in a user-defined fraction of the samples. Since the core features are a function of the fraction of samples that the feature must be observed in to be considered core, this is computed over a range of fractions defined by the `min_fraction`, `max_fraction`, and `steps` parameters. |
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55 |
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56 |
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57 | |
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58 |
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59 </help> |
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60 <citations> |
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61 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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62 </citations> |
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63 </tool> |