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changeset 0:359aa4321add draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:04:52 +0000
parents
children 54caf7f5c410
files qiime2__composition__tabulate.xml test-data/ancombc.test0.metadata.tsv test-data/ancombc.test0.table.qza test-data/ancombc.test1.metadata.tsv test-data/ancombc.test1.table.qza
diffstat 5 files changed, 131 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__composition__tabulate.xml	Fri Jan 13 22:04:52 2023 +0000
@@ -0,0 +1,59 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+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: 2022.11.1)
+for:
+    qiime2 (version: 2022.11.1)
+-->
+<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
+    <description> View tabular output from ANCOM-BC.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
+    </requirements>
+    <version_command>q2galaxy version composition</version_command>
+    <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required]  The ANCOM-BC output to be tabulated.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[DifferentialAbundance]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DifferentialAbundance]']</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: composition tabulate
+=============================
+ View tabular output from ANCOM-BC.
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+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.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.3402/mehd.v26.27663</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancombc.test0.metadata.tsv	Fri Jan 13 22:04:52 2023 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
+#q2:types	categorical	categorical	numeric	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
Binary file test-data/ancombc.test0.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancombc.test1.metadata.tsv	Fri Jan 13 22:04:52 2023 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
+#q2:types	categorical	categorical	numeric	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
Binary file test-data/ancombc.test1.table.qza has changed