Mercurial > repos > q2d2 > qiime2__diversity__alpha_group_significance

changeset 1:25b94f589fc8 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:44:33 +0000
parents d941f15652f0
children b7b5dc5a067b
files qiime2__diversity__alpha_group_significance.xml test-data/.gitkeep test-data/alpha_correlation.test0.alpha-div-faith-pd.qza test-data/alpha_correlation.test0.metadata.tsv test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza test-data/alpha_group_significance.test0.metadata.tsv
diffstat 5 files changed, 142 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__diversity__alpha_group_significance.xml	Mon Aug 29 19:38:39 2022 +0000
+++ b/qiime2__diversity__alpha_group_significance.xml	Fri Jan 13 22:44:33 2023 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, 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: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 diversity alpha-group-significance" id="qiime2__diversity__alpha_group_significance" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 diversity alpha-group-significance" id="qiime2__diversity__alpha_group_significance" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Alpha diversity comparisons</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version diversity</version_command>
-    <command detect_errors="aggressive">q2galaxy run diversity alpha_group_significance '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run diversity alpha_group_significance '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -45,7 +45,24 @@
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="alpha_diversity" value="alpha_group_significance.test0.alpha-div-faith-pd.qza" ftype="qza"/>
+            <repeat name="metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="alpha_group_significance.test0.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <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: diversity alpha-group-significance
 ===========================================
@@ -62,6 +79,24 @@
 ------------
 Visually and statistically compare groups of alpha diversity values.
 
+Examples:
+---------
+
+alpha_group_significance_faith_pd
+*********************************
+Using the ``qiime2 diversity alpha-group-significance`` tool:
+ #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza``
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Press the ``Execute`` button.
+
+
 
 |  
 
Binary file test-data/alpha_correlation.test0.alpha-div-faith-pd.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_correlation.test0.metadata.tsv	Fri Jan 13 22:44:33 2023 +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
Binary file test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_group_significance.test0.metadata.tsv	Fri Jan 13 22:44:33 2023 +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