--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__filter_seqs_length_by_taxon.xml	Thu Apr 25 21:24:57 2024 +0000
@@ -0,0 +1,85 @@
+<?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-seqs-length-by-taxon" id="qiime2__rescript__filter_seqs_length_by_taxon" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Filter sequences by length and taxonomic group.</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_seqs_length_by_taxon '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  Sequences to be filtered by length.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+        </param>
+        <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required]  Taxonomic classifications of sequences to be filtered.">
+            <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>
+        <repeat name="labels" min="1" help="[required]  One or more taxonomic labels to use for conditional filtering. For example, use this option to set different min/max filter settings for individual phyla. Must input the same number of labels as min_lens and/or max_lens. If a sequence matches multiple taxonomic labels, this method will apply the most stringent threshold(s): the longest minimum length and/or the shortest maximum length that is associated with the matching labels." title="labels: 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 name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="min_lens" help="[optional]  Minimum length thresholds to use for filtering sequences associated with each label. If any min_lens are specified, must have the same number of min_lens as labels. Sequences that contain this label in their taxonomy will be removed if they are less than the specified length." title="min_lens: List[Int % Range(1, None)]">
+                <param name="element" type="integer" min="1" value="" label="element: Int % Range(1, None)" help="[required]"/>
+            </repeat>
+            <repeat name="max_lens" help="[optional]  Maximum length thresholds to use for filtering sequences associated with each label. If any max_lens are specified, must have the same number of max_lens as labels. Sequences that contain this label in their taxonomy will be removed if they are more than the specified length." title="max_lens: List[Int % Range(1, None)]">
+                <param name="element" type="integer" min="1" value="" label="element: Int % Range(1, None)" help="[required]"/>
+            </repeat>
+            <param name="global_min" type="integer" min="1" optional="true" label="global_min: Int % Range(1, None)" help="[optional]  The minimum length threshold for filtering all sequences. Any sequence shorter than this length will be removed."/>
+            <param name="global_max" type="integer" min="1" optional="true" label="global_max: Int % Range(1, None)" help="[optional]  The maximum length threshold for filtering all sequences. Any sequence longer than this length will be removed."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="filtered_seqs" format="qza" label="${tool.name} on ${on_string}: filtered_seqs.qza" from_work_dir="filtered_seqs.qza"/>
+        <data name="discarded_seqs" format="qza" label="${tool.name} on ${on_string}: discarded_seqs.qza" from_work_dir="discarded_seqs.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript filter-seqs-length-by-taxon
+=============================================
+Filter sequences by length and taxonomic group.
+
+
+Outputs:
+--------
+:filtered_seqs.qza: Sequences that pass the filtering thresholds.
+:discarded_seqs.qza: Sequences that fall outside the filtering thresholds.
+
+|  
+
+Description:
+------------
+Filter sequences by length. Can filter both globally by minimum and/or maximum length, and set individual threshold for individual taxonomic groups (using the "labels" option). Note that filtering can be performed for multiple taxonomic groups simultaneously, and nested taxonomic filters can be applied (e.g., to apply a more stringent filter for a particular genus, but a less stringent filter for other members of the kingdom). For global length-based filtering without conditional taxonomic filtering, see filter_seqs_length.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>