Mercurial > repos > q2d2 > qiime2__vizard__boxplot
changeset 0:765052908e52 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 19:58:59 +0000 |
| parents | |
| children | |
| files | qiime2__vizard__boxplot.xml test-data/heatmap.test0.metadata.tsv test-data/lineplot.test0.metadata.tsv test-data/lineplot.test1.metadata.tsv test-data/lineplot.test2.metadata.tsv test-data/lineplot.test3.metadata.tsv test-data/lineplot.test4.metadata.tsv test-data/lineplot.test5.metadata.tsv test-data/scatterplot_2d.test0.metadata.tsv test-data/scatterplot_2d.test1.metadata.tsv |
| diffstat | 10 files changed, 307 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__vizard__boxplot.xml Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,118 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2024, 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: 2024.10.0) +for: + qiime2 (version: 2024.10.1) +--> +<tool name="qiime2 vizard boxplot" id="qiime2__vizard__boxplot" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Boxplot</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + </requirements> + <version_command>q2galaxy version vizard</version_command> + <command detect_errors="exit_code">q2galaxy run vizard boxplot '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <repeat name="metadata" min="1" help="[required] Any metadata-like input with at least one numeric measure and one categorical measure for visualizing." title="metadata: Metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" type="select" label="metadata: Metadata"> + <option value="tsv" selected="true">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + </when> + </conditional> + </repeat> + <param name="distribution_measure" type="text" label="distribution_measure: Str" help="[required] The numeric measure that will be used to create each box plot distribution."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="__q2galaxy__GUI__conditional__group_by__" label="group_by: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="group_by: Str" help="[optional] The categorical measure that will be used to group the data into separate box plots. If left blank, all data will be represented within a single box."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="group_by" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="group_by" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <param name="whisker_range" type="select" label="whisker_range: Str % Choices('tukeys_iqr', 'percentile', 'minmax')" display="radio"> + <option value="tukeys_iqr">tukeys_iqr</option> + <option value="percentile" selected="true">percentile</option> + <option value="minmax">minmax</option> + </param> + <param name="box_orientation" type="select" label="box_orientation: Str % Choices('horizontal', 'vertical')" display="radio"> + <option value="horizontal" selected="true">horizontal</option> + <option value="vertical">vertical</option> + </param> + <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional] The title of the boxplot."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="title" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="title" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + </section> + </inputs> + <outputs> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: vizard boxplot +======================= +Boxplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic boxplot for visualizing a numeric Metadata measure grouped by a categorical Metadata measure with choices for the whisker range. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.test0.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test0.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test1.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test2.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test3.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test4.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test5.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatterplot_2d.test0.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatterplot_2d.test1.metadata.tsv Wed Oct 30 19:58:59 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60