Mercurial > repos > q2d2 > qiime2__feature_table__tabulate_seqs
annotate qiime2__feature_table__tabulate_seqs.xml @ 4:9fe85eec5420 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 23:25:06 +0000 |
parents | 2feea4c63f4c |
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61ef9506af71
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'?> |
61ef9506af71
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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2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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4 |
61ef9506af71
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) |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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6 --> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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7 <!-- |
61ef9506af71
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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9fe85eec5420
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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9fe85eec5420
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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61ef9506af71
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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9fe85eec5420
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 tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> |
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61ef9506af71
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>View sequence associated with each feature</description> |
61ef9506af71
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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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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17 </requirements> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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18 <version_command>q2galaxy version feature_table</version_command> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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19 <command detect_errors="exit_code">q2galaxy run feature_table tabulate_seqs '$inputs'</command> |
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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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20 <configfiles> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 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__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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22 </configfiles> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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23 <inputs> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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24 <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated."> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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25 <options options_filter_attribute="metadata.semantic_type"> |
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9fe85eec5420
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit c7e80dcda727ce63b42aa8a946e9330310929797
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26 <filter type="add_value" value="FeatureData[Sequence]"/> |
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2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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27 <filter type="add_value" value="FeatureData[AlignedSequence]"/> |
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61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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28 </options> |
61ef9506af71
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator> |
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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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30 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> |
2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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32 <param name="taxonomy" type="data" format="qza" optional="true" label="taxonomy: Collection[FeatureData[Taxonomy]]" help="[optional] The taxonomic classifications of the tabulated features." multiple="true"> |
2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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33 <options options_filter_attribute="metadata.semantic_type"> |
2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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34 <filter type="add_value" value="FeatureData[Taxonomy]"/> |
2feea4c63f4c
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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35 </options> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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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__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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37 <repeat name="metadata" help="[optional] Any additional metadata for the tabulated features." title="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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38 <conditional name="__q2galaxy__GUI__conditional__metadata__"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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39 <param name="type" type="select" label="metadata: Metadata"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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40 <option value="tsv" selected="true">Metadata from TSV</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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41 <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__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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42 </param> |
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43 <when value="tsv"> |
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44 <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__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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45 </when> |
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46 <when value="qza"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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47 <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__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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48 </when> |
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49 </conditional> |
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50 </repeat> |
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51 <param name="merge_method" type="select" label="merge_method: Str % Choices('strict', 'union', 'intersect')" display="radio"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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52 <option value="strict" selected="true">strict</option> |
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53 <option value="union">union</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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54 <option value="intersect">intersect</option> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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55 </param> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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56 </section> |
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57 </inputs> |
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58 <outputs> |
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59 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> |
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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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60 </outputs> |
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61 <tests> |
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62 <test> |
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63 <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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64 <output name="visualization" ftype="qzv"> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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65 <assert_contents> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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66 <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__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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67 <has_line_matching expression="type: Visualization"/> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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68 </has_archive_member> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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69 </assert_contents> |
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70 </output> |
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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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71 </test> |
3
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72 <test> |
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73 <param name="data" value="tabulate_seqs.test1.rep-seqs-single-taxon.qza" ftype="qza"/> |
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74 <param name="taxonomy" value="tabulate_seqs.test1.single-taxonomy.qza" ftype="qza"/> |
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75 <output name="visualization" ftype="qzv"> |
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76 <assert_contents> |
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77 <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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78 <has_line_matching expression="type: Visualization"/> |
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79 </has_archive_member> |
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80 </assert_contents> |
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81 </output> |
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82 </test> |
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83 <test> |
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84 <param name="data" value="tabulate_seqs.test2.rep-seqs-multi-taxon.qza" ftype="qza"/> |
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85 <param name="taxonomy" value="tabulate_seqs.test2.multi-taxonomy/GG1.qza,tabulate_seqs.test2.multi-taxonomy/GG2.qza" ftype="qza"/> |
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86 <output name="visualization" ftype="qzv"> |
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87 <assert_contents> |
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88 <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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89 <has_line_matching expression="type: Visualization"/> |
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90 </has_archive_member> |
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91 </assert_contents> |
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92 </output> |
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93 </test> |
1
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94 </tests> |
0
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95 <help> |
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96 QIIME 2: feature-table tabulate-seqs |
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97 ==================================== |
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98 View sequence associated with each feature |
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99 |
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100 |
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101 Outputs: |
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102 -------- |
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103 :visualization.qzv: <no description> |
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104 |
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105 | |
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106 |
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107 Description: |
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108 ------------ |
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109 Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database. |
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110 |
1
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111 Examples: |
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112 --------- |
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113 |
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114 feature_table_tabulate_seqs |
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115 *************************** |
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116 Using the ``qiime2 feature-table tabulate-seqs`` tool: |
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117 #. Set *"data"* to ``#: rep-seqs.qza`` |
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118 #. Press the ``Execute`` button. |
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119 |
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120 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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121 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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122 |
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123 .. list-table:: |
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124 :align: left |
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125 :header-rows: 1 |
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126 |
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127 * - History Name |
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128 - *"Name"* to set (be sure to press ``Save``) |
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129 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv`` |
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130 - ``rep-seqs.qzv`` |
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131 |
3
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132 feature_table_tabulate_seqs_single_taxon |
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133 **************************************** |
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134 Using the ``qiime2 feature-table tabulate-seqs`` tool: |
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135 #. Set *"data"* to ``#: rep-seqs-single-taxon.qza`` |
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136 #. Expand the ``additional options`` section |
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137 |
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138 - Set *"taxonomy"* to ``#: ['single-taxonomy.qza']`` |
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139 |
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140 #. Press the ``Execute`` button. |
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141 |
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142 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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143 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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144 |
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145 .. list-table:: |
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146 :align: left |
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147 :header-rows: 1 |
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148 |
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149 * - History Name |
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150 - *"Name"* to set (be sure to press ``Save``) |
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151 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv`` |
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152 - ``rep-seqs.qzv`` |
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153 |
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154 feature_table_tabulate_seqs_multi_taxon |
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155 *************************************** |
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156 Using the ``qiime2 feature-table tabulate-seqs`` tool: |
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157 #. Set *"data"* to ``#: rep-seqs-multi-taxon.qza`` |
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158 #. Expand the ``additional options`` section |
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159 |
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160 - Set *"taxonomy"* to ``#: multi-taxonomy/`` |
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161 |
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162 #. Press the ``Execute`` button. |
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163 |
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164 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: |
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165 (Renaming is optional, but it will make any subsequent steps easier to complete.) |
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166 |
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167 .. list-table:: |
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168 :align: left |
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169 :header-rows: 1 |
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170 |
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171 * - History Name |
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172 - *"Name"* to set (be sure to press ``Save``) |
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173 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv`` |
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174 - ``rep-seqs.qzv`` |
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175 |
0
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176 |
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177 | |
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178 |
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179 </help> |
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180 <citations> |
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181 <citation type="doi">10.1093/nar/gkw1071</citation> |
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182 <citation type="doi">10.1093/nar/gkn201</citation> |
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183 <citation type="doi">10.1038/s41587-019-0209-9</citation> |
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184 </citations> |
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185 </tool> |