diff qiime2__deblur__denoise_16S.xml @ 1:2572fc0f88f2 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 69da7976573cc07a363ac66bdacc9269d7cd3732

--- a/qiime2__deblur__denoise_16S.xml	Mon Aug 29 19:25:20 2022 +0000
+++ b/qiime2__deblur__denoise_16S.xml	Fri Jan 13 22:42:34 2023 +0000
@@ -1,31 +1,31 @@
 <?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 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Deblur sequences using a 16S positive filter.</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 deblur</version_command>
-    <command detect_errors="aggressive">q2galaxy run deblur denoise_16S '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
     <inputs>
         <param name="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required]  The demultiplexed sequences to be denoised.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
                 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
-                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
             </options>
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
         </param>
@@ -47,7 +47,34 @@
         <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
         <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="demultiplexed_seqs" value="denoise_16S.test0.demux-filtered.qza" ftype="qza"/>
+            <param name="trim_length" value="120"/>
+            <param name="sample_stats" value="__q2galaxy__::literal::True"/>
+            <output name="representative_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: FeatureData\[Sequence\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="table" 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: FeatureTable\[Frequency\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="stats" 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: DeblurStats"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: deblur denoise-16S
 ===========================
@@ -66,6 +93,36 @@
 ------------
 Perform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter. Only forward reads are supported at this time. The specific reference used is the 88% OTUs from Greengenes 13_8. This mode of operation should only be used when data were generated from a 16S amplicon protocol on an Illumina platform. The reference is only used to assess whether each sequence is likely to be 16S by a local alignment using SortMeRNA with a permissive e-value; the reference is not used to characterize the sequences.
 
+Examples:
+---------
+
+denoise_16S
+***********
+Using the ``qiime2 deblur denoise-16S`` tool:
+ #. Set *"demultiplexed_seqs"* to ``#: demux-filtered.qza``
+ #. Set *"trim_length"* to ``120``
+ #. Expand the ``additional options`` section
+
+    - Set *"sample_stats"* to ``Yes``
+
+ #. 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 deblur denoise-16S [...] : table.qza``
+      - ``table.qza``
+    * - ``#: qiime2 deblur denoise-16S [...] : representative_sequences.qza``
+      - ``representative-sequences.qza``
+    * - ``#: qiime2 deblur denoise-16S [...] : stats.qza``
+      - ``denoising-stats.qza``
+
 
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