changeset 0:fd4dc4e33218 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__phylogeny__filter_tree.xml	Mon Aug 29 20:15:54 2022 +0000
@@ -0,0 +1,100 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 phylogeny filter-tree" id="qiime2__phylogeny__filter_tree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Remove features from tree based on metadata</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version phylogeny</version_command>
+    <command detect_errors="aggressive">q2galaxy run phylogeny filter_tree '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted¹ | Unrooted²]" help="[required]  Tree that should be filtered">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="Phylogeny[Unrooted]"/>
+                <filter type="add_value" value="Phylogeny[Rooted]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="table" type="data" format="qza" optional="true" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence | Composition]" help="[optional]  Feature table which contains the identifier that should be retained in the tree">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureTable[Composition]"/>
+                    <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                    <filter type="add_value" value="FeatureTable[Frequency]"/>
+                    <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[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+            </param>
+            <repeat name="metadata" help="[optional]  Feature metadata to use with the 'where' statement or to select tips to be retained. Metadata objects could also include FeatureData[Sequence] data types, if, forinstance, you want to filter to match represenative sequencces." 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>
+            <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional]  SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="where" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="where" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_tree" format="qza" label="${tool.name} on ${on_string}: filtered_tree.qza" from_work_dir="filtered_tree.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: phylogeny filter-tree
+==============================
+Remove features from tree based on metadata
+
+
+Outputs:
+--------
+:filtered_tree.qza: The resulting phylogenetic tree.
+
+|  
+
+Description:
+------------
+Remove tips from a tree if their identifiers based on a set of provided identifiers.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>