Mercurial > repos > q2d2 > qiime2__composition__ancombc

changeset 1:fe99db171ce5 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 19:34:16 +0000
parents 9b2a68d3017f
children 3bdf127442ed
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, 23 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__composition__ancombc.xml	Fri Jan 13 22:04:42 2023 +0000
+++ b/qiime2__composition__ancombc.xml	Thu Jun 08 19:34:16 2023 +0000
@@ -6,14 +6,14 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2022.11.1)
+    q2galaxy (version: 2023.5.0)
 for:
-    qiime2 (version: 2022.11.1)
+    qiime2 (version: 2023.5.1)
 -->
-<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">
+<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2023.5.0+q2galaxy.2023.5.0.2" 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>
+        <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 ancombc '$inputs'</command>
@@ -21,7 +21,7 @@
         <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.">
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table to be used for ANCOM-BC computation.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
             </options>
@@ -104,10 +104,13 @@
                     <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/>
                 </conditional>
             </repeat>
-            <param name="formula" value="bodysite + month"/>
+            <param name="formula" value="bodysite + animal"/>
             <repeat name="reference_levels">
                 <param name="element" value="bodysite::tongue"/>
             </repeat>
+            <repeat name="reference_levels">
+                <param name="element" value="animal::dog"/>
+            </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">
@@ -131,7 +134,7 @@
 
 Description:
 ------------
-ANCOM-BC description goes here.
+Apply Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) to identify features that are differentially abundant across groups.
 
 Examples:
 ---------
@@ -175,13 +178,13 @@
       #. Set *"Metadata Source"* to ``metadata.tsv``
 
 
- #. Set *"formula"* to ``bodysite + month``
+ #. Set *"formula"* to ``bodysite + animal``
  #. Expand the ``additional options`` section
 
-    - For *"reference_levels"*:
+    - For *"reference_levels"*, use the ``+ reference_levels`` button to add the corresponding values:
 
-      #. Set *"element"* to ``bodysite::tongue``
-      #. (Do not insert additional values.)
+      #. Add *"element"* set to ``bodysite::tongue``
+      #. Add *"element"* set to ``animal::dog``
 
 
  #. Press the ``Execute`` button.
@@ -203,7 +206,7 @@
 
 </help>
     <citations>
-        <citation type="doi">10.3402/mehd.v26.27663</citation>
+        <citation type="doi">10.1038/s41467-020-17041-7</citation>
         <citation type="doi">10.1038/s41587-019-0209-9</citation>
     </citations>
 </tool>
--- a/test-data/ancombc.test0.metadata.tsv	Fri Jan 13 22:04:42 2023 +0000
+++ b/test-data/ancombc.test0.metadata.tsv	Thu Jun 08 19:34:16 2023 +0000
@@ -1,5 +1,5 @@
 sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
-#q2:types	categorical	categorical	numeric	numeric	categorical	categorical	categorical	categorical	categorical
+#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
@@ -34,3 +34,6 @@
 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
--- a/test-data/ancombc.test1.metadata.tsv	Fri Jan 13 22:04:42 2023 +0000
+++ b/test-data/ancombc.test1.metadata.tsv	Thu Jun 08 19:34:16 2023 +0000
@@ -1,5 +1,5 @@
 sample-id	barcode-sequence	bodysite	month	day	subject	animal	testcolumn	singlecolumn	AZcolumn
-#q2:types	categorical	categorical	numeric	numeric	categorical	categorical	categorical	categorical	categorical
+#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
@@ -34,3 +34,6 @@
 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