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changeset 0:de8a1f53761e draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:34:23 +0000
parents
children c2690db851b5
files qiime2__composition__da_barplot.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, 190 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__composition__da_barplot.xml	Thu Jun 08 19:34:23 2023 +0000
@@ -0,0 +1,112 @@
+<?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: 2023.5.0)
+for:
+    qiime2 (version: 2023.5.1)
+-->
+<tool name="qiime2 composition da-barplot" id="qiime2__composition__da_barplot" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+    <description>Differential abundance bar plots</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2023.5</container>
+    </requirements>
+    <version_command>q2galaxy version composition</version_command>
+    <command detect_errors="exit_code">q2galaxy run composition da_barplot '$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 plotted.">
+            <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>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="effect_size_label" type="text" value="lfc" label="effect_size_label: Str" help="[default: 'lfc']  Label for effect sizes in `data`.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="feature_id_label" type="text" value="id" label="feature_id_label: Str" help="[default: 'id']  Label for feature ids in `data`.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="error_label" type="text" value="se" label="error_label: Str" help="[default: 'se']  Label for effect size errors in `data`.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="significance_label" type="text" value="q_val" label="significance_label: Str" help="[default: 'q_val']  Label for statistical significance level in `data`.">
+                <sanitizer>
+                    <valid initial="string.printable"/>
+                </sanitizer>
+            </param>
+            <param name="significance_threshold" type="float" min="0.0" max="1.0" value="1.0" label="significance_threshold: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 1.0]  Exclude features with statistical significance level greater (i.e., less significant) than this threshold."/>
+            <param name="effect_size_threshold" type="float" min="0.0" value="0.0" label="effect_size_threshold: Float % Range(0.0, None)" help="[default: 0.0]  Exclude features with an absolute value of effect size less than this threshold."/>
+            <repeat name="feature_ids" help="[optional]  Exclude features if their ids are not included in this index." title="feature_ids: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__feature_ids__">
+                    <param name="type" type="select" label="feature_ids: 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>
+            <conditional name="__q2galaxy__GUI__conditional__level_delimiter__" label="level_delimiter: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="level_delimiter: Str" help="[optional]  If feature ids encode hierarchical information, split the levels when generating feature labels in the visualization using this delimiter.">
+                    <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="level_delimiter" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="level_delimiter" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </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 da-barplot
+===============================
+Differential abundance bar plots
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Generate bar plot views of ANCOM-BC output. One plot will be present per column in the ANCOM-BC output. The `significance_threshold`, `effect_size_threshold` and `feature_ids` filter results are intersected, such that only features that remain after all three filters have been applied will be present in the output.
+
+
+|  
+
+</help>
+    <citations>
+        <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	Thu Jun 08 19:34:23 2023 +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/ancombc.test0.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ancombc.test1.metadata.tsv	Thu Jun 08 19:34:23 2023 +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/ancombc.test1.table.qza has changed