Mercurial > repos > q2d2 > qiime2__metadata__tabulate

changeset 2:d6e1b976c373 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:49:32 +0000
parents f6763a86190b
children b833fbd936a7
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, 5 insertions(+), 142 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__metadata__tabulate.xml	Fri Jan 13 22:58:11 2023 +0000
+++ b/qiime2__metadata__tabulate.xml	Thu Jun 08 19:49:32 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 metadata tabulate" id="qiime2__metadata__tabulate" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 metadata tabulate" id="qiime2__metadata__tabulate" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
     <description>Interactively explore Metadata in an HTML table</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.11</container>
+        <container type="docker">quay.io/qiime2/core:2023.5</container>
     </requirements>
     <version_command>q2galaxy version metadata</version_command>
     <command detect_errors="exit_code">q2galaxy run metadata tabulate '$inputs'</command>
@@ -42,45 +42,7 @@
     <outputs>
         <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
     </outputs>
-    <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>
+    <tests/>
     <help>
 QIIME 2: metadata tabulate
 ==========================
@@ -97,69 +59,6 @@
 ------------
 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
--- a/test-data/tabulate.test1.sample-metadata.tsv	Fri Jan 13 22:58:11 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-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