Mercurial > repos > q2d2 > qiime2__vizard__lineplot
changeset 0:df9f1ff48c29 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 19:59:34 +0000 |
| parents | |
| children | |
| files | qiime2__vizard__lineplot.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, 585 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__vizard__lineplot.xml Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,396 @@ +<?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 lineplot" id="qiime2__vizard__lineplot" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Lineplot</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 lineplot '$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 two numeric measures 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="x_measure" type="text" label="x_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the x-axis."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + <param name="y_measure" type="text" label="y_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the y-axis."> + <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"> + <param name="replicate_method" type="select" label="replicate_method: Str % Choices('none', 'median', 'mean')" display="radio"> + <option value="none" selected="true">none</option> + <option value="median">median</option> + <option value="mean">mean</option> + </param> + <conditional name="__q2galaxy__GUI__conditional__group_by__" label="group_by: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="group_by: Str" help="[optional] Categorical measure from the input Metadata that should be used for grouping the lineplot."> + <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> + <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 lineplot."> + <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> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="x"/> + <param name="y_measure" value="y"/> + <param name="replicate_method" value="median"/> + <param name="group_by" value="group"/> + <param name="title" value="Lineplot with median replicate method__comma__ grouped by `group`."/> + <output name="visualization" ftype="qzv"/> + </test> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test1.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="x"/> + <param name="y_measure" value="y"/> + <param name="replicate_method" value="mean"/> + <param name="group_by" value="group"/> + <param name="title" value="Lineplot with mean replicate method__comma__ grouped by `group`."/> + <output name="visualization" ftype="qzv"/> + </test> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test2.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="x"/> + <param name="y_measure" value="y"/> + <param name="replicate_method" value="median"/> + <param name="title" value="Lineplot with median replicate method (no grouping)."/> + <output name="visualization" ftype="qzv"/> + </test> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test3.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="x"/> + <param name="y_measure" value="y"/> + <param name="replicate_method" value="mean"/> + <param name="title" value="Lineplot with mean replicate method (no grouping)."/> + <output name="visualization" ftype="qzv"/> + </test> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test4.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="a"/> + <param name="y_measure" value="y"/> + <param name="group_by" value="group"/> + <param name="title" value="Lineplot with no replicate method__comma__ grouped by `group`."/> + <output name="visualization" ftype="qzv"/> + </test> + <test> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="lineplot.test5.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="x_measure" value="b"/> + <param name="y_measure" value="y"/> + <param name="title" value="Lineplot with no replicate method (no grouping)."/> + <output name="visualization" ftype="qzv"/> + </test> + </tests> + <help> +QIIME 2: vizard lineplot +======================== +Lineplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen `x_measure` remains fixed. + +Examples: +--------- + +lineplot_median_replicates_with_grouping +**************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_with_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_median_replicates_no_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"title"* to ``Lineplot with median replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_no_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_with_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``a`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_no_grouping +********************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``b`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + - Set *"title"* to ``Lineplot with no replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + + +| + +</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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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 19:59:34 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