diff qiime2__cutadapt__demux_paired.xml @ 1:d58b93d0a723 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 69da7976573cc07a363ac66bdacc9269d7cd3732

--- a/qiime2__cutadapt__demux_paired.xml	Mon Aug 29 19:22:08 2022 +0000
+++ b/qiime2__cutadapt__demux_paired.xml	Fri Jan 13 22:41:52 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 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex paired-end sequence data with barcodes in-sequence.</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 cutadapt</version_command>
-    <command detect_errors="aggressive">q2galaxy run cutadapt demux_paired '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -77,7 +77,30 @@
         <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
         <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="seqs" value="demux_paired.test0.seqs.qza" ftype="qza"/>
+            <conditional name="forward_barcodes">
+                <param name="type" value="tsv"/>
+                <param name="source" value="demux_paired.test0.md.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\[PairedEndSequencesWithQuality\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="untrimmed_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: MultiplexedPairedEndBarcodeInSequence"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: cutadapt demux-paired
 ==============================
@@ -95,6 +118,22 @@
 ------------
 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or a separate barcode file).
 
+Examples:
+---------
+
+paired
+******
+Using the ``qiime2 cutadapt demux-paired`` tool:
+ #. Set *"seqs"* to ``#: seqs.qza``
+ #. For *"forward_barcodes"*:
+
+    #. Leave as ``Metadata from TSV``
+    #. Set *"Metadata Source"* to ``md.tsv``
+    #. Set *"Column Name"* to ``barcode-sequence``
+
+ #. Press the ``Execute`` button.
+
+
 
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