diff qiime2__demux__emp_single.xml @ 1:335abb486193 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732

--- a/qiime2__demux__emp_single.xml	Mon Aug 29 19:27:37 2022 +0000
+++ b/qiime2__demux__emp_single.xml	Fri Jan 13 22:43:21 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 demux emp-single" id="qiime2__demux__emp_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 demux emp-single" id="qiime2__demux__emp_single" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex sequence data generated with the EMP protocol.</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 demux</version_command>
-    <command detect_errors="aggressive">q2galaxy run demux emp_single '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run demux emp_single '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -58,7 +58,30 @@
         <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
         <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="seqs" value="emp_single.test0.sequences.qza" ftype="qza"/>
+            <conditional name="barcodes">
+                <param name="type" value="tsv"/>
+                <param name="source" value="emp_single.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
+                <param name="column" value="2"/>
+            </conditional>
+            <output name="per_sample_sequences" 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: SampleData\[SequencesWithQuality\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="error_correction_details" 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: ErrorCorrectionDetails"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: demux emp-single
 =========================
@@ -76,6 +99,35 @@
 ------------
 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/
 
+Examples:
+---------
+
+demux
+*****
+Using the ``qiime2 demux emp-single`` tool:
+ #. Set *"seqs"* to ``#: sequences.qza``
+ #. For *"barcodes"*:
+
+    #. Leave as ``Metadata from TSV``
+    #. Set *"Metadata Source"* to ``sample-metadata.tsv``
+    #. Set *"Column Name"* to ``barcode-sequence``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for each 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 demux emp-single [...] : per_sample_sequences.qza``
+      - ``demux.qza``
+    * - ``#: qiime2 demux emp-single [...] : error_correction_details.qza``
+      - ``demux-details.qza``
+
 
 |