# HG changeset patch
# User q2d2
# Date 1730318281 0
# Node ID 0699c24331f42e92123324c8c0033a20fe5fe178

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats commit 5f71b597c9495eae67a447744fded834f56ca1f7

diff -r 000000000000 -r 0699c24331f4 qiime2__stats__plot_rainclouds.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__stats__plot_rainclouds.xml	Wed Oct 30 19:58:01 2024 +0000
@@ -0,0 +1,110 @@
+<?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 stats plot-rainclouds" id="qiime2__stats__plot_rainclouds" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Raincloud plots</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 stats</version_command>
+    <command detect_errors="exit_code">q2galaxy run stats plot_rainclouds '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="data" type="data" format="qza" label="data: Dist1D[Multi | Ordered | Unordered | NestedOrdered | NestedUnordered, Matched | Independent]" help="[required]  The group distributions to plot.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="Dist1D[NestedOrdered, Matched]"/>
+                <filter type="add_value" value="Dist1D[Ordered, Matched]"/>
+                <filter type="add_value" value="Dist1D[Ordered, Independent]"/>
+                <filter type="add_value" value="Dist1D[Multi, Independent]"/>
+                <filter type="add_value" value="Dist1D[NestedOrdered, Independent]"/>
+                <filter type="add_value" value="Dist1D[Multi, Matched]"/>
+                <filter type="add_value" value="Dist1D[Unordered, Matched]"/>
+                <filter type="add_value" value="Dist1D[Unordered, Independent]"/>
+                <filter type="add_value" value="Dist1D[NestedUnordered, Matched]"/>
+                <filter type="add_value" value="Dist1D[NestedUnordered, Independent]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Independent]', 'Dist1D[Multi, Matched]', 'Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]', 'Dist1D[Ordered, Independent]', 'Dist1D[Ordered, Matched]', 'Dist1D[Unordered, Independent]', 'Dist1D[Unordered, Matched]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="stats" type="data" format="qza" optional="true" label="stats: StatsTable[Pairwise]" help="[optional]  Statistical tests to display.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="StatsTable[Pairwise]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['StatsTable[Pairwise]']</validator>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="data" value="plot_rainclouds.test0.dist.qza" ftype="qza"/>
+            <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}\/metadata.yaml">
+                        <has_line_matching expression="type: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: stats plot-rainclouds
+==============================
+Raincloud plots
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Plot raincloud distributions for each group.
+
+Examples:
+---------
+
+plot_rainclouds
+***************
+Using the ``qiime2 stats plot-rainclouds`` tool:
+ #. Set *"data"* to ``#: dist.qza``
+ #. 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 stats plot-rainclouds [...] : visualization.qzv``
+      - ``raincloud-plot.qzv``
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 0699c24331f4 test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza
Binary file test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/alpha_group_significance.test0.metadata.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_group_significance.test0.metadata.tsv	Wed Oct 30 19:58:01 2024 +0000
@@ -0,0 +1,50 @@
+sample_name	barcode	mouse_id	genotype	cage_id	donor	donor_status	days_post_transplant	genotype_and_donor_status
+#q2:types	categorical	categorical	categorical	categorical	categorical	categorical	numeric	categorical
+recip.220.WT.OB1.D7	CCTCCGTCATGG	457	wild type	C35	hc_1	Healthy	49	wild type and Healthy
+recip.290.ASO.OB2.D1	AACAGTAAACAA	456	susceptible	C35	hc_1	Healthy	49	susceptible and Healthy
+recip.389.WT.HC2.D21	ATGTATCAATTA	435	susceptible	C31	hc_1	Healthy	21	susceptible and Healthy
+recip.391.ASO.PD2.D14	GTCAGTATGGCT	435	susceptible	C31	hc_1	Healthy	14	susceptible and Healthy
+recip.391.ASO.PD2.D21	AGACAGTAGGAG	437	susceptible	C31	hc_1	Healthy	21	susceptible and Healthy
+recip.391.ASO.PD2.D7	GGTCTTAGCACC	435	susceptible	C31	hc_1	Healthy	7	susceptible and Healthy
+recip.400.ASO.HC2.D14	CGTTCGCTAGCC	437	susceptible	C31	hc_1	Healthy	14	susceptible and Healthy
+recip.401.ASO.HC2.D7	ATTTACAATTGA	437	susceptible	C31	hc_1	Healthy	7	susceptible and Healthy
+recip.403.ASO.PD2.D21	CGCAGATTAGTA	456	susceptible	C35	hc_1	Healthy	21	susceptible and Healthy
+recip.411.ASO.HC2.D14	ATGTTAGGGAAT	456	susceptible	C35	hc_1	Healthy	14	susceptible and Healthy
+recip.411.ASO.HC2.D21	CTCATATGCTAT	457	wild type	C35	hc_1	Healthy	21	wild type and Healthy
+recip.411.ASO.HC2.D49	GCAACGAACGAG	435	susceptible	C31	hc_1	Healthy	49	susceptible and Healthy
+recip.412.ASO.HC2.D14	AAGTGGCTATCC	457	wild type	C35	hc_1	Healthy	14	wild type and Healthy
+recip.412.ASO.HC2.D7	GCATTCGGCGTT	456	susceptible	C35	hc_1	Healthy	7	susceptible and Healthy
+recip.413.WT.HC2.D7	ACCAGTGACTCA	457	wild type	C35	hc_1	Healthy	7	wild type and Healthy
+recip.456.ASO.HC3.D49	ACGGCGTTATGT	468	wild type	C42	hc_1	Healthy	49	wild type and Healthy
+recip.458.ASO.HC3.D21	ACGGCCCTGGAG	468	wild type	C42	hc_1	Healthy	21	wild type and Healthy
+recip.458.ASO.HC3.D49	CATTTGACGACG	469	wild type	C42	hc_1	Healthy	49	wild type and Healthy
+recip.459.WT.HC3.D14	ACATGGGCGGAA	468	wild type	C42	hc_1	Healthy	14	wild type and Healthy
+recip.459.WT.HC3.D21	CATAAATTCTTG	469	wild type	C42	hc_1	Healthy	21	wild type and Healthy
+recip.459.WT.HC3.D49	GCTGCGTATACC	536	susceptible	C43	pd_1	PD	49	susceptible and PD
+recip.460.WT.HC3.D14	CTGCGGATATAC	469	wild type	C42	hc_1	Healthy	14	wild type and Healthy
+recip.460.WT.HC3.D21	GTCAATTAGTGG	536	susceptible	C43	pd_1	PD	21	susceptible and PD
+recip.460.WT.HC3.D49	GAGAAGCTTATA	537	wild type	C43	pd_1	PD	49	wild type and PD
+recip.460.WT.HC3.D7	GACCCGTTTCGC	468	wild type	C42	hc_1	Healthy	7	wild type and Healthy
+recip.461.ASO.HC3.D21	AGCCCGCAAAGG	537	wild type	C43	pd_1	PD	21	wild type and PD
+recip.461.ASO.HC3.D49	GGCGTAACGGCA	538	wild type	C44	pd_1	PD	49	wild type and PD
+recip.461.ASO.HC3.D7	ATTGCCTTGATT	469	wild type	C42	hc_1	Healthy	7	wild type and Healthy
+recip.462.WT.PD3.D14	GTGAGGGCAAGT	536	susceptible	C43	pd_1	PD	14	susceptible and PD
+recip.462.WT.PD3.D21	GGCCTATAAGTC	538	wild type	C44	pd_1	PD	21	wild type and PD
+recip.462.WT.PD3.D49	AATACAGACCTG	539	susceptible	C44	pd_1	PD	49	susceptible and PD
+recip.462.WT.PD3.D7	TTAGGATTCTAT	536	susceptible	C43	pd_1	PD	7	susceptible and PD
+recip.463.WT.PD3.D14	ATATTGGCAGCC	537	wild type	C43	pd_1	PD	14	wild type and PD
+recip.463.WT.PD3.D21	CGCGGCGCAGCT	539	susceptible	C44	pd_1	PD	21	susceptible and PD
+recip.463.WT.PD3.D7	GTTTATCTTAAG	537	wild type	C43	pd_1	PD	7	wild type and PD
+recip.464.WT.PD3.D14	TCATCCGTCGGC	538	wild type	C44	pd_1	PD	14	wild type and PD
+recip.465.ASO.PD3.D14	GGCTTCGGAGCG	539	susceptible	C44	pd_1	PD	14	susceptible and PD
+recip.465.ASO.PD3.D7	CAGTCTAGTACG	538	wild type	C44	pd_1	PD	7	wild type and PD
+recip.466.ASO.PD3.D7	GTGGGACTGCGC	539	susceptible	C44	pd_1	PD	7	susceptible and PD
+recip.467.WT.HC3.D49.a	GTCAGGTGCGGC	437	susceptible	C31	hc_1	Healthy	49	susceptible and Healthy
+recip.467.WT.HC3.D49.b	GTTAACTTACTA	546	susceptible	C49	pd_1	PD	49	susceptible and PD
+recip.536.ASO.PD4.D49	CAAATTCGGGAT	547	wild type	C49	pd_1	PD	49	wild type and PD
+recip.537.WT.PD4.D21	CTCTATTCCACC	546	susceptible	C49	pd_1	PD	21	susceptible and PD
+recip.538.WT.PD4.D21	ATGGATAGCTAA	547	wild type	C49	pd_1	PD	21	wild type and PD
+recip.539.ASO.PD4.D14	GATCCGGCAGGA	546	susceptible	C49	pd_1	PD	14	susceptible and PD
+recip.539.ASO.PD4.D7	GTTCGAGTGAAT	546	susceptible	C49	pd_1	PD	7	susceptible and PD
+recip.540.ASO.HC4.D14	CTTCCAACTCAT	547	wild type	C49	pd_1	PD	14	wild type and PD
+recip.540.ASO.HC4.D7	CGGCCTAAGTTC	547	wild type	C49	pd_1	PD	7	wild type and PD
diff -r 000000000000 -r 0699c24331f4 test-data/mann_whitney_u.test0.refdist.qza
Binary file test-data/mann_whitney_u.test0.refdist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/mann_whitney_u.test0.timedist.qza
Binary file test-data/mann_whitney_u.test0.timedist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/mann_whitney_u_facet.test0.dist.qza
Binary file test-data/mann_whitney_u_facet.test0.dist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/mann_whitney_u_facet.test1.dist.qza
Binary file test-data/mann_whitney_u_facet.test1.dist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/plot_rainclouds.test0.dist.qza
Binary file test-data/plot_rainclouds.test0.dist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/wilcoxon_srt.test0.timedist.qza
Binary file test-data/wilcoxon_srt.test0.timedist.qza has changed
diff -r 000000000000 -r 0699c24331f4 test-data/wilcoxon_srt_facet.test0.dist.qza
Binary file test-data/wilcoxon_srt_facet.test0.dist.qza has changed