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changeset 0:9b2a68d3017f 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 22:04:42 +0000
parents
children fe99db171ce5
files qiime2__composition__ancombc.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, 281 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__composition__ancombc.xml	Fri Jan 13 22:04:42 2023 +0000
@@ -0,0 +1,209 @@
+<?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 ancombc" id="qiime2__composition__ancombc" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Analysis of Composition of Microbiomes with Bias Correction</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 ancombc '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to be used for ANCOM computation.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <repeat name="metadata" min="1" help="[required]  The sample metadata." 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>
+        <param name="formula" type="text" label="formula: Str" help="[required]  How the microbial absolute abundances for each taxon depend on the variables within the `metadata`.">
+            <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>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="p_adj_method" type="select" label="p_adj_method: Str % Choices('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')">
+                <option value="holm" selected="true">holm</option>
+                <option value="hochberg">hochberg</option>
+                <option value="hommel">hommel</option>
+                <option value="bonferroni">bonferroni</option>
+                <option value="BH">BH</option>
+                <option value="BY">BY</option>
+                <option value="fdr">fdr</option>
+                <option value="none">none</option>
+            </param>
+            <param name="prv_cut" type="float" value="0.1" label="prv_cut: Float" help="[default: 0.1]  A numerical fraction between 0-1. Taxa with prevalences less than this value will be excluded from the analysis."/>
+            <param name="lib_cut" type="integer" value="0" label="lib_cut: Int" help="[default: 0]  A numerical threshold for filtering samples based on library sizes. Samples with library sizes less than this value will be excluded from the analysis."/>
+            <repeat name="reference_levels" help="[optional]  Define the reference level(s) to be used for categorical columns found in the `formula`. These categorical factors are dummy coded relative to the reference(s) provided. The syntax is as follows: &quot;column_name::column_value&quot;" title="reference_levels: 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>
+            <param name="neg_lb" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="neg_lb: Bool" help="[default: No]  Whether to classify a taxon as a structural zero using its asymptotic lower bound."/>
+            <param name="tol" type="float" value="1e-05" label="tol: Float" help="[default: 1e-05]  The iteration convergence tolerance for the E-M algorithm."/>
+            <param name="max_iter" type="integer" value="100" label="max_iter: Int" help="[default: 100]  The maximum number of iterations for the E-M algorithm."/>
+            <param name="conserve" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="conserve: Bool" help="[default: No]  Whether to use a conservative variance estimator for the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large."/>
+            <param name="alpha" type="float" value="0.05" label="alpha: Float" help="[default: 0.05]  Level of significance."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="differentials" format="qza" label="${tool.name} on ${on_string}: differentials.qza" from_work_dir="differentials.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="ancombc.test0.table.qza" ftype="qza"/>
+            <repeat name="metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="ancombc.test0.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="formula" value="bodysite"/>
+            <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="table" value="ancombc.test1.table.qza" ftype="qza"/>
+            <repeat name="metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="formula" value="bodysite + month"/>
+            <repeat name="reference_levels">
+                <param name="element" value="bodysite::tongue"/>
+            </repeat>
+            <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: composition ancombc
+============================
+Analysis of Composition of Microbiomes with Bias Correction
+
+
+Outputs:
+--------
+:differentials.qza: The calculated per-feature differentials.
+
+|  
+
+Description:
+------------
+ANCOM-BC description goes here.
+
+Examples:
+---------
+
+ancombc_single_formula
+**********************
+Using the ``qiime2 composition ancombc`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Set *"formula"* to ``bodysite``
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 composition ancombc [...] : differentials.qza``
+      - ``dataloaf.qza``
+
+ancombc_multi_formula_with_reference_levels
+*******************************************
+Using the ``qiime2 composition ancombc`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Set *"formula"* to ``bodysite + month``
+ #. Expand the ``additional options`` section
+
+    - For *"reference_levels"*:
+
+      #. Set *"element"* to ``bodysite::tongue``
+      #. (Do not insert additional values.)
+
+
+ #. Press the ``Execute`` button.
+
+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 composition ancombc [...] : differentials.qza``
+      - ``dataloaf.qza``
+
+
+|  
+
+</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 22:04:42 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 22:04:42 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