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changeset 0:acada7129b61 draft default tip

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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 19:59:12 +0000
parents
children
files qiime2__vizard__scatterplot_2d.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, 405 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__vizard__scatterplot_2d.xml	Wed Oct 30 19:59:12 2024 +0000
@@ -0,0 +1,216 @@
+<?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 scatterplot-2d" id="qiime2__vizard__scatterplot_2d" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>2D Scatterplot</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 scatterplot_2d '$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>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__x_measure__" label="x_measure: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="x_measure: Str" help="[optional]  Numeric measure from the input Metadata that should be plotted on the x-axis.">
+                    <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="x_measure" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="x_measure" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__y_measure__" label="y_measure: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="y_measure: Str" help="[optional]  Numeric measure from the input Metadata that should be plotted on the y-axis.">
+                    <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="y_measure" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="y_measure" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__color_by__" label="color_by: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="color_by: Str" help="[optional]  Categorical measure from the input Metadata that should be used for color-coding the scatterplot.">
+                    <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="color_by" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="color_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 scatterplot.">
+                    <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="scatterplot_2d.test0.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <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="scatterplot_2d.test1.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="x_measure" value="x"/>
+            <param name="y_measure" value="y"/>
+            <param name="color_by" value="group"/>
+            <output name="visualization" ftype="qzv"/>
+        </test>
+    </tests>
+    <help>
+QIIME 2: vizard scatterplot-2d
+==============================
+2D Scatterplot
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Basic 2D scatterplot for visualizing two numeric Metadata measures with optional categorical color grouping.
+
+Examples:
+---------
+
+scatterplot_defaults
+********************
+Using the ``qiime2 vizard scatterplot-2d`` tool:
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. 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 scatterplot-2d [...] : visualization.qzv``
+      - ``scatterplot.qzv``
+
+scatterplot_all_measures
+************************
+Using the ``qiime2 vizard scatterplot-2d`` tool:
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Expand the ``additional options`` section
+
+    #. Set *"x_measure"* to ``x``
+    #. Set *"y_measure"* to ``y``
+    #. Set *"color_by"* to ``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 scatterplot-2d [...] : visualization.qzv``
+      - ``scatterplot.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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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 19:59:12 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