Galaxy |

Changeset 0:55fd8d766006 (2022-08-29)

Next changeset 1:bea0cdf2d9c8 (2023-01-13)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

added:
qiime2__longitudinal__volatility.xml
test-data/.gitkeep

diff -r 000000000000 -r 55fd8d766006 qiime2__longitudinal__volatility.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__longitudinal__volatility.xml Mon Aug 29 20:10:48 2022 +0000

[

b'@@ -0,0 +1,135 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">\n+ <description>Generate interactive volatility plot</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version longitudinal</version_command>\n+ <command detect_errors="aggressive">q2galaxy run longitudinal volatility \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." title="metadata: Metadata">\n+ <conditional name="__q2galaxy__GUI__conditional__metadata__">\n+ <param name="type" type="select" label="metadata: Metadata">\n+ <option value="tsv" selected="true">Metadata from TSV</option>\n+ <option value="qza">Metadata from Artifact</option>\n+ </param>\n+ <when value="tsv">\n+ <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>\n+ </when>\n+ <when value="qza">\n+ <param name="source" type="data" format="qza" label="Metadata Source"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ <param name="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information.">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table containing metrics.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'FeatureTable[RelativeFrequency]\']</validator>\n+ </param>\n+ <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional] Metadata column containing IDs for individual subjects.">\n+ <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>\n+ <option value="__q2galaxy__::control::provide">Provide a value</option>\n+ </param>\n+ <when value="__q2galaxy__::control::default">\n+ <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/>\n+ </when>\n+ <when value="__q2galaxy__::control::provide">\n+ <param name="individual_id_column" type="text">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ '..b'ditional__default_group_column__" label="default_group_column: Str">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="default_group_column: Str" help="[optional] The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization).">\n+ <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>\n+ <option value="__q2galaxy__::control::provide">Provide a value</option>\n+ </param>\n+ <when value="__q2galaxy__::control::default">\n+ <param name="default_group_column" type="hidden" value="__q2galaxy__::literal::None"/>\n+ </when>\n+ <when value="__q2galaxy__::control::provide">\n+ <param name="default_group_column" type="text">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ <conditional name="__q2galaxy__GUI__conditional__default_metric__" label="default_metric: Str">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="default_metric: Str" help="[optional] Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).">\n+ <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>\n+ <option value="__q2galaxy__::control::provide">Provide a value</option>\n+ </param>\n+ <when value="__q2galaxy__::control::default">\n+ <param name="default_metric" type="hidden" value="__q2galaxy__::literal::None"/>\n+ </when>\n+ <when value="__q2galaxy__::control::provide">\n+ <param name="default_metric" type="text">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ </param>\n+ </when>\n+ </conditional>\n+ <param name="yscale" type="select" label="yscale: Str % Choices(\'linear\', \'pow\', \'sqrt\', \'log\')" display="radio">\n+ <option value="linear" selected="true">linear</option>\n+ <option value="pow">pow</option>\n+ <option value="sqrt">sqrt</option>\n+ <option value="log">log</option>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: longitudinal volatility\n+================================\n+Generate interactive volatility plot\n+\n+\n+Outputs:\n+--------\n+:visualization.qzv: <no description>\n+\n+| \n+\n+Description:\n+------------\n+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.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1128/mSystems.00219-18</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'