| Previous changeset 1:bea0cdf2d9c8 (2023-01-13) Next changeset 3:085340f69dfe (2024-04-25) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 65e4952f33eb335528e8553150e9097e5ea8f556 |
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modified:
qiime2__longitudinal__volatility.xml |
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added:
test-data/volatility.test0.metadata.tsv |
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removed:
test-data/.gitkeep |
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| diff -r bea0cdf2d9c8 -r 0e3d1b6523e2 qiime2__longitudinal__volatility.xml --- a/qiime2__longitudinal__volatility.xml Fri Jan 13 22:57:39 2023 +0000 +++ b/qiime2__longitudinal__volatility.xml Thu Jun 08 19:48:47 2023 +0000 |
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| @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2022.11.1) + q2galaxy (version: 2023.5.0) for: - qiime2 (version: 2022.11.1) + qiime2 (version: 2023.5.1) --> -<tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Generate interactive volatility plot</description> <requirements> - <container type="docker">quay.io/qiime2/core:2022.11</container> + <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version longitudinal</version_command> <command detect_errors="exit_code">q2galaxy run longitudinal volatility '$inputs'</command> @@ -107,7 +107,24 @@ <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> </outputs> - <tests/> + <tests> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="volatility.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="state_column" value="month"/> + <output name="visualization" ftype="qzv"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/data\/index.html"> + <has_line_matching expression="^\s*"month": null,$"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: longitudinal volatility ================================ @@ -124,6 +141,35 @@ ------------ Generate an interactive control chart depicting the longitudinal volatility of sample metadata and/or feature frequencies across time (as set using the "state_column" parameter). Any numeric metadata column (and metadata-transformable artifacts, e.g., alpha diversity results) can be plotted on the y-axis, and are selectable using the "metric_column" selector. Metric values are averaged to compare across any categorical metadata column using the "group_column" selector. Longitudinal volatility for individual subjects sampled over time is co-plotted as "spaghetti" plots if the "individual_id_column" parameter is used. state_column will typically be a measure of time, but any numeric metadata column can be used. +Examples: +--------- + +longitudinal_volatility +*********************** +Using the ``qiime2 longitudinal volatility`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"state_column"* to ``month`` + #. 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 longitudinal volatility [...] : visualization.qzv`` + - ``volatility-plot.qzv`` + | |
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| diff -r bea0cdf2d9c8 -r 0e3d1b6523e2 test-data/volatility.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/volatility.test0.metadata.tsv Thu Jun 08 19:48:47 2023 +0000 |
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| b'@@ -0,0 +1,877 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