Mercurial > repos > q2d2 > qiime2__metadata__tabulate

changeset 1:f6763a86190b draft

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__metadata commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:58:11 +0000
parents b85efa8e40a0
children d6e1b976c373
files qiime2__metadata__tabulate.xml test-data/.gitkeep test-data/tabulate.test0.demux-stats.qza test-data/tabulate.test1.faith-pd-vector.qza test-data/tabulate.test1.sample-metadata.tsv
diffstat 4 files changed, 144 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__metadata__tabulate.xml	Mon Aug 29 20:13:07 2022 +0000
+++ b/qiime2__metadata__tabulate.xml	Fri Jan 13 22:58:11 2023 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+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: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Interactively explore Metadata in an HTML table</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version metadata</version_command>
-    <command detect_errors="aggressive">q2galaxy run metadata tabulate '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run metadata tabulate '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -42,7 +42,45 @@
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <repeat name="input">
+                <conditional name="__q2galaxy__GUI__conditional__input__">
+                    <param name="type" value="qza"/>
+                    <param name="source" value="tabulate.test0.demux-stats.qza" ftype="qza"/>
+                </conditional>
+            </repeat>
+            <output name="visualization" ftype="qzv">
+                <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: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <repeat name="input">
+                <conditional name="__q2galaxy__GUI__conditional__input__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="tabulate.test1.sample-metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <repeat name="input">
+                <conditional name="__q2galaxy__GUI__conditional__input__">
+                    <param name="type" value="qza"/>
+                    <param name="source" value="tabulate.test1.faith-pd-vector.qza" ftype="qza"/>
+                </conditional>
+            </repeat>
+            <param name="page_size" value="25"/>
+            <output name="visualization" ftype="qzv">
+                <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: Visualization"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: metadata tabulate
 ==========================
@@ -59,6 +97,69 @@
 ------------
 Generate a tabular view of Metadata. The output visualization supports interactive filtering, sorting, and exporting to common file formats.
 
+Examples:
+---------
+
+basic_tabulate_usage
+********************
+Using the ``qiime2 metadata tabulate`` tool:
+ #. For *"input"*:
+
+    - Perform the following steps.
+
+      #. Change to ``Metadata from Artifact``
+      #. Set *"Metadata Source"* to ``demux-stats.qza``
+
+
+ #. 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 metadata tabulate [...] : visualization.qzv``
+      - ``demux-stats-viz.qzv``
+
+tabulate_multiple_files
+***********************
+| Multiple metadata files or artifacts viewed as metadata can be merged to make one tabular visualization. This one displays only 25 metadata rows per page.
+Using the ``qiime2 metadata tabulate`` tool:
+ #. For *"input"*:
+
+    #. Perform the following steps.
+
+       #. Leave as ``Metadata from TSV``
+       #. Set *"Metadata Source"* to ``sample-metadata.tsv``
+
+    #. Press the ``+ Insert input`` button to set up the next steps.
+
+       #. Change to ``Metadata from Artifact``
+       #. Set *"Metadata Source"* to ``faith-pd-vector.qza``
+
+
+ #. Expand the ``additional options`` section
+
+    - Set *"page_size"* to ``25``
+
+ #. 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 metadata tabulate [...] : visualization.qzv``
+      - ``demux-stats-viz.qzv``
+
 
 |  
 
Binary file test-data/tabulate.test0.demux-stats.qza has changed
Binary file test-data/tabulate.test1.faith-pd-vector.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabulate.test1.sample-metadata.tsv	Fri Jan 13 22:58:11 2023 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168