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Changeset 0:0eea854dbf4d (2022-08-29)

Next changeset 1:c75e3e049c2f (2023-01-13)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

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+++ b/qiime2__diversity_lib__observed_features.xml Mon Aug 29 19:42:40 2022 +0000

[

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+<?xml version='1.0' encoding='utf-8'?>
+
+
+<tool name="qiime2 diversity-lib observed-features" id="qiime2__diversity_lib__observed_features" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Observed Features</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version diversity_lib</version_command>
+    <command detect_errors="aggressive">q2galaxy run diversity_lib observed_features '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples for which the number of observed features should be calculated. Table values will be converted to presence/absence.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="observed_features.test0.feature-table.qza" ftype="qza"/>
+            <output name="vector" 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\[AlphaDiversity\]"/>
+                    </has_archive_member>
+                    <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}\/data\/alpha-diversity.tsv">
+                        <has_line_matching expression="S1	1"/>
+                        <has_line_matching expression="S2	1"/>
+                        <has_line_matching expression="S3	2"/>
+                        <has_line_matching expression="S4	2"/>
+                        <has_line_matching expression="S5	3"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: diversity-lib observed-features
+========================================
+Observed Features
+
+
+Outputs:
+--------
+:vector.qza: Vector containing per-sample counts of observed features.
+
+|
+
+Description:
+------------
+Compute the number of observed features for each sample in a feature table
+
+Examples:
+---------
+
+basic
+*****
+Using the ``qiime2 diversity-lib observed-features`` tool:
+ #. Set *"table"* to ``#: feature-table.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 diversity-lib observed-features [...] : vector.qza``
+      - ``obs-feat-vector.qza``
+
+
+|
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>

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