changeset 0:1b1fd5ca308b draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__filter_taxa.xml	Thu Apr 25 21:19:31 2024 +0000
@@ -0,0 +1,91 @@
+<?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 rescript filter-taxa" id="qiime2__rescript__filter_taxa" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Filter taxonomy by list of IDs or search criteria.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version rescript</version_command>
+    <command detect_errors="exit_code">q2galaxy run rescript filter_taxa '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required]  Taxonomy to filter.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Taxonomy]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="ids_to_keep" help="[optional]  List of IDs to keep (as Metadata). Selecting these IDs occurs after inclusion and exclusion filtering." title="ids_to_keep: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__ids_to_keep__">
+                    <param name="type" type="select" label="ids_to_keep: 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>
+            <repeat name="include" help="[optional]  List of search terms. Taxa containing one or more of these terms will be retained. Inclusion filtering occurs prior to exclusion filtering and selecting `ids_to_keep`." title="include: List[Str]">
+                <param name="element" type="text" label="element: Str" help="[required]">
+                    <sanitizer>
+                        <valid initial="string.printable"/>
+                    </sanitizer>
+                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+                </param>
+            </repeat>
+            <repeat name="exclude" help="[optional]  List of search terms. Taxa containing one or more of these terms will be excluded. Exclusion filtering occurs after inclusion filtering and prior to selecting `ids_to_keep`." title="exclude: List[Str]">
+                <param name="element" type="text" label="element: Str" help="[required]">
+                    <sanitizer>
+                        <valid initial="string.printable"/>
+                    </sanitizer>
+                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
+                </param>
+            </repeat>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_taxonomy" format="qza" label="${tool.name} on ${on_string}: filtered_taxonomy.qza" from_work_dir="filtered_taxonomy.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript filter-taxa
+=============================
+Filter taxonomy by list of IDs or search criteria.
+
+
+Outputs:
+--------
+:filtered_taxonomy.qza: The filtered taxonomy.
+
+|  
+
+Description:
+------------
+Filter taxonomy by list of IDs or search criteria.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>