# HG changeset patch
# User q2d2
# Date 1730318219 0
# Node ID c7ae38450ff970c6736ce938ecba1f2de67a9e39

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

diff -r 000000000000 -r c7ae38450ff9 qiime2__stats__prep_alpha_distribution.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__stats__prep_alpha_distribution.xml	Wed Oct 30 19:56:59 2024 +0000
@@ -0,0 +1,133 @@
+<?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 prep-alpha-distribution" id="qiime2__stats__prep_alpha_distribution" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Alpha diversity to Dist1D</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 prep_alpha_distribution '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required]  Alpha diversity which will become the &quot;measure&quot;">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[AlphaDiversity]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator>
+        </param>
+        <repeat name="metadata" min="1" help="[required]  Sample metadata to use" 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>
+        <repeat name="columns" min="1" help="[required]  Columns to include as group information" title="columns: List[Str]">
+            <param name="element" type="text" label="element: Str" help="[required]">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+                <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+            </param>
+        </repeat>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__subject__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="subject: Str % Choices('')¹'³ | Str²'⁴" help="[default: '']  If provided, will cause the Dist1D to be matched for repeated measures.">
+                    <option value="" selected="true"> (Str)</option>
+                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
+                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
+                </param>
+                <when value="">
+                    <param name="subject" type="hidden" value=""/>
+                </when>
+                <when value="__q2galaxy__::control::Str">
+                    <param name="subject" type="text" value="" label="subject: Str" help="[default: '']  If provided, will cause the Dist1D to be matched for repeated measures.">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+                <when value="__q2galaxy__::control::Str">
+                    <param name="subject" type="text" value="" label="subject: Str" help="[default: '']  If provided, will cause the Dist1D to be matched for repeated measures.">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__timepoint__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="timepoint: Str % Choices('')¹'² | Str³'⁴" help="[default: '']  If provided, will cause the Dist1D to be stratified by timepoint. Required if using ``subject``.">
+                    <option value="" selected="true"> (Str)</option>
+                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
+                    <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>
+                </param>
+                <when value="">
+                    <param name="timepoint" type="hidden" value=""/>
+                </when>
+                <when value="__q2galaxy__::control::Str">
+                    <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: '']  If provided, will cause the Dist1D to be stratified by timepoint. Required if using ``subject``.">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+                <when value="__q2galaxy__::control::Str">
+                    <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: '']  If provided, will cause the Dist1D to be stratified by timepoint. Required if using ``subject``.">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="distribution" format="qza" label="${tool.name} on ${on_string}: distribution.qza" from_work_dir="distribution.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: stats prep-alpha-distribution
+======================================
+Alpha diversity to Dist1D
+
+
+Outputs:
+--------
+:distribution.qza: The resulting Dist1D.
+
+|  
+
+Description:
+------------
+Alpha diversity to Dist1D
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r c7ae38450ff9 test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza
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diff -r 000000000000 -r c7ae38450ff9 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 19:56:59 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
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