# HG changeset patch
# User q2d2
# Date 1730318291 0
# Node ID 3cbec5fc30ad62fcc4637b037eea3529f4946ec6

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

diff -r 000000000000 -r 3cbec5fc30ad qiime2__stats__wilcoxon_srt.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__stats__wilcoxon_srt.xml	Wed Oct 30 19:58:11 2024 +0000
@@ -0,0 +1,127 @@
+<?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 wilcoxon-srt" id="qiime2__stats__wilcoxon_srt" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Wilcoxon Signed Rank Test</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 wilcoxon_srt '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="distribution" type="data" format="qza" label="distribution: Dist1D[Ordered, Matched]" help="[required]">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="Dist1D[Ordered, Matched]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Ordered, Matched]']</validator>
+        </param>
+        <param name="compare" type="select" label="compare: Str % Choices('baseline', 'consecutive')" display="radio">
+            <option value="__q2galaxy__::literal::None">Selection required</option>
+            <option value="baseline">baseline</option>
+            <option value="consecutive">consecutive</option>
+            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__baseline_group__" label="baseline_group: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="baseline_group: Str" help="[optional]  If &quot;baseline&quot; is the selected comparison, this is the column that will be used to compare all other groups against.">
+                    <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="baseline_group" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="baseline_group" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param name="alternative" type="select" label="alternative: Str % Choices('two-sided', 'greater', 'less')" display="radio">
+                <option value="two-sided" selected="true">two-sided</option>
+                <option value="greater">greater</option>
+                <option value="less">less</option>
+            </param>
+            <param name="p_val_approx" type="select" label="p_val_approx: Str % Choices('auto', 'exact', 'asymptotic')" display="radio">
+                <option value="auto" selected="true">auto</option>
+                <option value="exact">exact</option>
+                <option value="asymptotic">asymptotic</option>
+            </param>
+            <param name="ignore_empty_comparator" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_empty_comparator: Bool" help="[default: No]  Ignore any group that does not have any overlapping subjects with comparison group. These groups will have NaNs in the stats table output"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="distribution" value="wilcoxon_srt.test0.timedist.qza" ftype="qza"/>
+            <param name="compare" value="baseline"/>
+            <param name="baseline_group" value="0"/>
+            <param name="p_val_approx" value="asymptotic"/>
+            <output name="stats" ftype="qza">
+                <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: StatsTable\[Pairwise\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: stats wilcoxon-srt
+===========================
+Wilcoxon Signed Rank Test
+
+
+Outputs:
+--------
+:stats.qza: The Wilcoxon SRT table for either the "baseline" or "consecutive" comparison.
+
+|  
+
+Description:
+------------
+
+
+Examples:
+---------
+
+wilcoxon_baseline0
+******************
+Using the ``qiime2 stats wilcoxon-srt`` tool:
+ #. Set *"distribution"* to ``#: timedist.qza``
+ #. Set *"compare"* to ``baseline``
+ #. Expand the ``additional options`` section
+
+    #. Set *"baseline_group"* to ``0``
+    #. Set *"p_val_approx"* to ``asymptotic``
+
+ #. Press the ``Execute`` button.
+
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">https://doi.org/10.2307/3001968</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 3cbec5fc30ad test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza
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diff -r 000000000000 -r 3cbec5fc30ad 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 19:58:11 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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