Mercurial > repos > q2d2 > qiime2__composition__tabulate

changeset 5:600f11a2839d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 18:41:25 +0000
parents cb1a60431256
children
files qiime2__composition__tabulate.xml test-data/ancombc.test0.table.qza test-data/ancombc.test1.table.qza test-data/ancombc2.test0.metadata.tsv test-data/ancombc2.test0.table.qza test-data/ancombc2.test1.metadata.tsv test-data/ancombc2.test1.table.qza
diffstat 7 files changed, 89 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__composition__tabulate.xml	Wed Oct 30 19:36:12 2024 +0000
+++ b/qiime2__composition__tabulate.xml	Mon May 05 18:41:25 2025 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2024, QIIME 2 development team.
+Copyright (c) 2025, 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)
+    q2galaxy (version: 2025.4.0)
 for:
-    qiime2 (version: 2024.10.1)
+    qiime2 (version: 2025.4.0)
 -->
-<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
-    <description> View tabular output from ANCOM-BC.</description>
+<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
+    <description> View tabular output from ANCOM-BC or ANCOM-BC2.</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
     </requirements>
     <version_command>q2galaxy version composition</version_command>
     <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command>
@@ -24,11 +24,12 @@
         <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
-        <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required]  The ANCOM-BC output to be tabulated.">
+        <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance | ANCOMBC2Output]" help="[required]  The ANCOM-BC or ANCOM-BC2 output to be tabulated.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[ANCOMBC2Output]"/>
                 <filter type="add_value" value="FeatureData[DifferentialAbundance]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DifferentialAbundance]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[ANCOMBC2Output]', 'FeatureData[DifferentialAbundance]']</validator>
         </param>
     </inputs>
     <outputs>
@@ -38,7 +39,7 @@
     <help>
 QIIME 2: composition tabulate
 =============================
- View tabular output from ANCOM-BC.
+ View tabular output from ANCOM-BC or ANCOM-BC2.
 
 
 Outputs:
@@ -49,7 +50,7 @@
 
 Description:
 ------------
-Generate tabular view of ANCOM-BC output, which includes per-page views for the log-fold change (lfc), standard error (se), P values, Q values, and W scores.
+Generate tabular view of ANCOM-BC or ANCOM-BC2 output, which includes per-page views for the log-fold change (lfc), standard error (se), P values, Q values, and W scores.
 
 
 |  
Binary file test-data/ancombc.test0.table.qza has changed
Binary file test-data/ancombc.test1.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancombc2.test0.metadata.tsv	Mon May 05 18:41:25 2025 +0000
@@ -0,0 +1,39 @@
+sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
+#q2:types	categorical	categorical	categorical	numeric	categorical	categorical	categorical	categorical	categorical
+L1S8	AGCTGACTAGTC	gut	10	28	subject-1	dog	test1	value	A
+L1S57	ACACACTATGGC	gut	1	20	subject-1	dog	test2	value	Z
+L1S76	ACTACGTGTGGT	gut	2	17	subject-1	cow	test1	value	Z
+L1S105	AGTGCGATGCGT	gut	3	17	subject-1	cat	test2	value	A
+L2S155	ACGATGCGACCA	left palm	1	20	subject-1	cat	test1	value	A
+L2S175	AGCTATCCACGA	left palm	2	17	subject-1	cat	test2	value	A
+L2S204	ATGCAGCTCAGT	left palm	3	17	subject-1	bird	test1	value	Z
+L2S222	CACGTGACATGT	left palm	4	14	subject-1	cow	test2	value	Z
+L3S242	ACAGTTGCGCGA	right palm	10	28	subject-1	bird	test1	value	A
+L3S294	CACGACAGGCTA	right palm	1	20	subject-1	dog	test2	value	Z
+L3S313	AGTGTCACGGTG	right palm	2	17	subject-1	dog	test1	value	Z
+L3S341	CAAGTGAGAGAG	right palm	3	17	subject-1	cat	test2	value	Z
+L3S360	CATCGTATCAAC	right palm	4	14	subject-1	cat	test1	value	A
+L5S104	CAGTGTCAGGAC	tongue	10	28	subject-1	bird	test2	value	A
+L5S155	ATCTTAGACTGC	tongue	1	20	subject-1	cow	test1	value	Z
+L5S174	CAGACATTGCGT	tongue	2	17	subject-1	dog	test2	value	A
+L5S203	CGATGCACCAGA	tongue	3	17	subject-1	cat	test1	value	Z
+L5S222	CTAGAGACTCTT	tongue	4	14	subject-1	bird	test2	value	Z
+L1S140	ATGGCAGCTCTA	gut	10	28	subject-2	dog	test1	value	Z
+L1S208	CTGAGATACGCG	gut	1	20	subject-2	dog	test2	value	A
+L1S257	CCGACTGAGATG	gut	3	17	subject-2	dog	test1	value	A
+L1S281	CCTCTCGTGATC	gut	4	14	subject-2	cat	test2	value	Z
+L2S240	CATATCGCAGTT	left palm	10	28	subject-2	cat	test1	value	A
+L2S309	CGTGCATTATCA	left palm	1	20	subject-2	cat	test2	value	A
+L2S357	CTAACGCAGTCA	left palm	3	17	subject-2	bird	test1	value	Z
+L2S382	CTCAATGACTCA	left palm	4	14	subject-2	bird	test2	value	A
+L3S378	ATCGATCTGTGG	right palm	10	28	subject-2	cow	test1	value	Z
+L4S63	CTCGTGGAGTAG	right palm	1	20	subject-2	dog	test2	value	Z
+L4S112	GCGTTACACACA	right palm	3	17	subject-2	cat	test1	value	A
+L4S137	GAACTGTATCTC	right palm	4	14	subject-2	bird	test2	value	A
+L5S240	CTGGACTCATAG	tongue	10	28	subject-2	dog	test1	value	A
+L6S93	GCGTTACACACA	tongue	3	17	subject-2	dog	test1	value	Z
+L6S20	GAACTGTATCTC	tongue	4	14	subject-2	bird	test2	value	Z
+L6S68	CTGGACTCATAG	gut	10	28	subject-2	cow	test1	value	Z
+L6SD93	GCGTTACACACA	toe	3	17	subject-2	dog	test1	value	
+L6SD20	GAACTGTATCTC	toe	4	14	subject-2	bird	test2	value	
+L6SD68	CTGGACTCATAG	toe	10	28	subject-2	cow	test1	value	
Binary file test-data/ancombc2.test0.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancombc2.test1.metadata.tsv	Mon May 05 18:41:25 2025 +0000
@@ -0,0 +1,39 @@
+sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
+#q2:types	categorical	categorical	categorical	numeric	categorical	categorical	categorical	categorical	categorical
+L1S8	AGCTGACTAGTC	gut	10	28	subject-1	dog	test1	value	A
+L1S57	ACACACTATGGC	gut	1	20	subject-1	dog	test2	value	Z
+L1S76	ACTACGTGTGGT	gut	2	17	subject-1	cow	test1	value	Z
+L1S105	AGTGCGATGCGT	gut	3	17	subject-1	cat	test2	value	A
+L2S155	ACGATGCGACCA	left palm	1	20	subject-1	cat	test1	value	A
+L2S175	AGCTATCCACGA	left palm	2	17	subject-1	cat	test2	value	A
+L2S204	ATGCAGCTCAGT	left palm	3	17	subject-1	bird	test1	value	Z
+L2S222	CACGTGACATGT	left palm	4	14	subject-1	cow	test2	value	Z
+L3S242	ACAGTTGCGCGA	right palm	10	28	subject-1	bird	test1	value	A
+L3S294	CACGACAGGCTA	right palm	1	20	subject-1	dog	test2	value	Z
+L3S313	AGTGTCACGGTG	right palm	2	17	subject-1	dog	test1	value	Z
+L3S341	CAAGTGAGAGAG	right palm	3	17	subject-1	cat	test2	value	Z
+L3S360	CATCGTATCAAC	right palm	4	14	subject-1	cat	test1	value	A
+L5S104	CAGTGTCAGGAC	tongue	10	28	subject-1	bird	test2	value	A
+L5S155	ATCTTAGACTGC	tongue	1	20	subject-1	cow	test1	value	Z
+L5S174	CAGACATTGCGT	tongue	2	17	subject-1	dog	test2	value	A
+L5S203	CGATGCACCAGA	tongue	3	17	subject-1	cat	test1	value	Z
+L5S222	CTAGAGACTCTT	tongue	4	14	subject-1	bird	test2	value	Z
+L1S140	ATGGCAGCTCTA	gut	10	28	subject-2	dog	test1	value	Z
+L1S208	CTGAGATACGCG	gut	1	20	subject-2	dog	test2	value	A
+L1S257	CCGACTGAGATG	gut	3	17	subject-2	dog	test1	value	A
+L1S281	CCTCTCGTGATC	gut	4	14	subject-2	cat	test2	value	Z
+L2S240	CATATCGCAGTT	left palm	10	28	subject-2	cat	test1	value	A
+L2S309	CGTGCATTATCA	left palm	1	20	subject-2	cat	test2	value	A
+L2S357	CTAACGCAGTCA	left palm	3	17	subject-2	bird	test1	value	Z
+L2S382	CTCAATGACTCA	left palm	4	14	subject-2	bird	test2	value	A
+L3S378	ATCGATCTGTGG	right palm	10	28	subject-2	cow	test1	value	Z
+L4S63	CTCGTGGAGTAG	right palm	1	20	subject-2	dog	test2	value	Z
+L4S112	GCGTTACACACA	right palm	3	17	subject-2	cat	test1	value	A
+L4S137	GAACTGTATCTC	right palm	4	14	subject-2	bird	test2	value	A
+L5S240	CTGGACTCATAG	tongue	10	28	subject-2	dog	test1	value	A
+L6S93	GCGTTACACACA	tongue	3	17	subject-2	dog	test1	value	Z
+L6S20	GAACTGTATCTC	tongue	4	14	subject-2	bird	test2	value	Z
+L6S68	CTGGACTCATAG	gut	10	28	subject-2	cow	test1	value	Z
+L6SD93	GCGTTACACACA	toe	3	17	subject-2	dog	test1	value	
+L6SD20	GAACTGTATCTC	toe	4	14	subject-2	bird	test2	value	
+L6SD68	CTGGACTCATAG	toe	10	28	subject-2	cow	test1	value	
Binary file test-data/ancombc2.test1.table.qza has changed