diff qiime2__feature_table__summarize_plus.xml @ 0:4954486b6f4c draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_table__summarize_plus.xml	Thu Apr 25 21:08:12 2024 +0000
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+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2024, 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: 2024.2.1)
+for:
+    qiime2 (version: 2024.2.0)
+-->
+<tool name="qiime2 feature-table summarize-plus" id="qiime2__feature_table__summarize_plus" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Summarize table plus</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="exit_code">q2galaxy run feature_table summarize_plus '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence]" help="[required]  The feature table to be summarized.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="metadata" help="[optional]  The sample metadata." title="metadata: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" type="select" label="metadata: Metadata">
+                        <option value="tsv" selected="true">Metadata from TSV</option>
+                        <option value="qza">Metadata from Artifact</option>
+                    </param>
+                    <when value="tsv">
+                        <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                    </when>
+                    <when value="qza">
+                        <param name="source" type="data" format="qza" label="Metadata Source"/>
+                    </when>
+                </conditional>
+            </repeat>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="feature_frequencies" format="qza" label="${tool.name} on ${on_string}: feature_frequencies.qza" from_work_dir="feature_frequencies.qza"/>
+        <data name="sample_frequencies" format="qza" label="${tool.name} on ${on_string}: sample_frequencies.qza" from_work_dir="sample_frequencies.qza"/>
+        <data name="summary" format="qzv" label="${tool.name} on ${on_string}: summary.qzv" from_work_dir="summary.qzv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="summarize_plus.test0.feature-table.qza" ftype="qza"/>
+            <output name="feature_frequencies" 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: ImmutableMetadata"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="sample_frequencies" 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: ImmutableMetadata"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="summary" 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: feature-table summarize-plus
+=====================================
+Summarize table plus
+
+
+Outputs:
+--------
+:feature_frequencies.qza: Per-sample and total frequencies per feature.
+:sample_frequencies.qza: Observed feature count and total frequencies per sample.
+:summary.qzv: Visual summary of feature table
+
+|  
+
+Description:
+------------
+Generate visual and tabular summaries of a feature table. Tabulate sample and feature frequencies.
+
+Examples:
+---------
+
+feature_table_summarize_plus
+****************************
+Using the ``qiime2 feature-table summarize-plus`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. 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 feature-table summarize-plus [...] : feature_frequencies.qza``
+      - ``feature-frequencies.qza``
+    * - ``#: qiime2 feature-table summarize-plus [...] : sample_frequencies.qza``
+      - ``sample-frequencies.qza``
+    * - ``#: qiime2 feature-table summarize-plus [...] : summary.qzv``
+      - ``visual summary.qzv``
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>