Mercurial > repos > q2d2 > qiime2__feature_table__tabulate_seqs

annotate qiime2__feature_table__tabulate_seqs.xml @ 2:6d5cd7bcc0d0 draft

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author q2d2
date Thu, 08 Jun 2023 19:44:24 +0000
parents 38b618d1eb4d
children 2feea4c63f4c
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2023, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 feature-table tabulate-seqs" id="qiime2__feature_table__tabulate_seqs" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>View sequence associated with each feature</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</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 tabulate_seqs '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="data" type="data" format="qza" label="data: FeatureData[Sequence | AlignedSequence]" help="[required] The feature sequences to be tabulated.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Sequence]"/>
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27 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
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28 </options>
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]', 'FeatureData[Sequence]']</validator>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="data" value="tabulate_seqs.test0.rep-seqs.qza" ftype="qza"/>
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38 <output name="visualization" ftype="qzv">
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39 <assert_contents>
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40 <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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41 <has_line_matching expression="type: Visualization"/>
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42 </has_archive_member>
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47 <help>
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48 QIIME 2: feature-table tabulate-seqs
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49 ====================================
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50 View sequence associated with each feature
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51
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52
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53 Outputs:
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54 --------
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55 :visualization.qzv: &lt;no description&gt;
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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 Generate tabular view of feature identifier to sequence mapping, including links to BLAST each sequence against the NCBI nt database.
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62
1
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63 Examples:
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64 ---------
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65
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66 feature_table_tabulate_seqs
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67 ***************************
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68 Using the ``qiime2 feature-table tabulate-seqs`` tool:
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69 #. Set *"data"* to ``#: rep-seqs.qza``
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70 #. Press the ``Execute`` button.
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71
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72 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
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73 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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74
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75 .. list-table::
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76 :align: left
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77 :header-rows: 1
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78
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79 * - History Name
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80 - *"Name"* to set (be sure to press ``Save``)
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81 * - ``#: qiime2 feature-table tabulate-seqs [...] : visualization.qzv``
38b618d1eb4d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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82 - ``rep-seqs.qzv``
38b618d1eb4d planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 69da7976573cc07a363ac66bdacc9269d7cd3732
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83
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84
61ef9506af71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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85 |
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86
61ef9506af71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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87 </help>
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88 <citations>
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89 <citation type="doi">10.1093/nar/gkw1071</citation>
61ef9506af71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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90 <citation type="doi">10.1093/nar/gkn201</citation>
61ef9506af71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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91 <citation type="doi">10.1038/s41587-019-0209-9</citation>
61ef9506af71 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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92 </citations>
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93 </tool>