| Previous changeset 0:b85efa8e40a0 (2022-08-29) Next changeset 2:d6e1b976c373 (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__metadata__tabulate.xml |
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added:
test-data/tabulate.test0.demux-stats.qza test-data/tabulate.test1.faith-pd-vector.qza test-data/tabulate.test1.sample-metadata.tsv |
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removed:
test-data/.gitkeep |
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| diff -r b85efa8e40a0 -r f6763a86190b qiime2__metadata__tabulate.xml --- a/qiime2__metadata__tabulate.xml Mon Aug 29 20:13:07 2022 +0000 +++ b/qiime2__metadata__tabulate.xml Fri Jan 13 22:58:11 2023 +0000 |
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| @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.8.1) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Interactively explore Metadata in an HTML table</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.8</container> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version metadata</version_command> - <command detect_errors="aggressive">q2galaxy run metadata tabulate '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run metadata tabulate '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -42,7 +42,45 @@ <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> </outputs> - <tests/> + <tests> + <test> + <repeat name="input"> + <conditional name="__q2galaxy__GUI__conditional__input__"> + <param name="type" value="qza"/> + <param name="source" value="tabulate.test0.demux-stats.qza" ftype="qza"/> + </conditional> + </repeat> + <output name="visualization" ftype="qzv"> + <assert_contents> + <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"> + <has_line_matching expression="type: Visualization"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <test> + <repeat name="input"> + <conditional name="__q2galaxy__GUI__conditional__input__"> + <param name="type" value="tsv"/> + <param name="source" value="tabulate.test1.sample-metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <repeat name="input"> + <conditional name="__q2galaxy__GUI__conditional__input__"> + <param name="type" value="qza"/> + <param name="source" value="tabulate.test1.faith-pd-vector.qza" ftype="qza"/> + </conditional> + </repeat> + <param name="page_size" value="25"/> + <output name="visualization" ftype="qzv"> + <assert_contents> + <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"> + <has_line_matching expression="type: Visualization"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: metadata tabulate ========================== @@ -59,6 +97,69 @@ ------------ Generate a tabular view of Metadata. The output visualization supports interactive filtering, sorting, and exporting to common file formats. +Examples: +--------- + +basic_tabulate_usage +******************** +Using the ``qiime2 metadata tabulate`` tool: + #. For *"input"*: + + - Perform the following steps. + + #. Change to ``Metadata from Artifact`` + #. Set *"Metadata Source"* to ``demux-stats.qza`` + + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 metadata tabulate [...] : visualization.qzv`` + - ``demux-stats-viz.qzv`` + +tabulate_multiple_files +*********************** +| Multiple metadata files or artifacts viewed as metadata can be merged to make one tabular visualization. This one displays only 25 metadata rows per page. +Using the ``qiime2 metadata tabulate`` tool: + #. For *"input"*: + + #. Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``sample-metadata.tsv`` + + #. Press the ``+ Insert input`` button to set up the next steps. + + #. Change to ``Metadata from Artifact`` + #. Set *"Metadata Source"* to ``faith-pd-vector.qza`` + + + #. Expand the ``additional options`` section + + - Set *"page_size"* to ``25`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 metadata tabulate [...] : visualization.qzv`` + - ``demux-stats-viz.qzv`` + | |
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| diff -r b85efa8e40a0 -r f6763a86190b test-data/tabulate.test1.sample-metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabulate.test1.sample-metadata.tsv Fri Jan 13 22:58:11 2023 +0000 |
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| @@ -0,0 +1,36 @@ +sample-id barcode-sequence body-site year month day subject reported-antibiotic-usage days-since-experiment-start +#q2:types categorical categorical numeric numeric numeric categorical categorical numeric +L1S8 AGCTGACTAGTC gut 2008 10 28 subject-1 Yes 0 +L1S57 ACACACTATGGC gut 2009 1 20 subject-1 No 84 +L1S76 ACTACGTGTGGT gut 2009 2 17 subject-1 No 112 +L1S105 AGTGCGATGCGT gut 2009 3 17 subject-1 No 140 +L2S155 ACGATGCGACCA left palm 2009 1 20 subject-1 No 84 +L2S175 AGCTATCCACGA left palm 2009 2 17 subject-1 No 112 +L2S204 ATGCAGCTCAGT left palm 2009 3 17 subject-1 No 140 +L2S222 CACGTGACATGT left palm 2009 4 14 subject-1 No 168 +L3S242 ACAGTTGCGCGA right palm 2008 10 28 subject-1 Yes 0 +L3S294 CACGACAGGCTA right palm 2009 1 20 subject-1 No 84 +L3S313 AGTGTCACGGTG right palm 2009 2 17 subject-1 No 112 +L3S341 CAAGTGAGAGAG right palm 2009 3 17 subject-1 No 140 +L3S360 CATCGTATCAAC right palm 2009 4 14 subject-1 No 168 +L5S104 CAGTGTCAGGAC tongue 2008 10 28 subject-1 Yes 0 +L5S155 ATCTTAGACTGC tongue 2009 1 20 subject-1 No 84 +L5S174 CAGACATTGCGT tongue 2009 2 17 subject-1 No 112 +L5S203 CGATGCACCAGA tongue 2009 3 17 subject-1 No 140 +L5S222 CTAGAGACTCTT tongue 2009 4 14 subject-1 No 168 +L1S140 ATGGCAGCTCTA gut 2008 10 28 subject-2 Yes 0 +L1S208 CTGAGATACGCG gut 2009 1 20 subject-2 No 84 +L1S257 CCGACTGAGATG gut 2009 3 17 subject-2 No 140 +L1S281 CCTCTCGTGATC gut 2009 4 14 subject-2 No 168 +L2S240 CATATCGCAGTT left palm 2008 10 28 subject-2 Yes 0 +L2S309 CGTGCATTATCA left palm 2009 1 20 subject-2 No 84 +L2S357 CTAACGCAGTCA left palm 2009 3 17 subject-2 No 140 +L2S382 CTCAATGACTCA left palm 2009 4 14 subject-2 No 168 +L3S378 ATCGATCTGTGG right palm 2008 10 28 subject-2 Yes 0 +L4S63 CTCGTGGAGTAG right palm 2009 1 20 subject-2 No 84 +L4S112 GCGTTACACACA right palm 2009 3 17 subject-2 No 140 +L4S137 GAACTGTATCTC right palm 2009 4 14 subject-2 No 168 +L5S240 CTGGACTCATAG tongue 2008 10 28 subject-2 Yes 0 +L6S20 GAGGCTCATCAT tongue 2009 1 20 subject-2 No 84 +L6S68 GATACGTCCTGA tongue 2009 3 17 subject-2 No 140 +L6S93 GATTAGCACTCT tongue 2009 4 14 subject-2 No 168 |