# HG changeset patch
# User q2d2
# Date 1714080279 0
# Node ID 2eff5d70ecd5d6786a6a4d354a4bd0e8a4ec8e77

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

diff -r 000000000000 -r 2eff5d70ecd5 qiime2__rescript__trim_alignment.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__trim_alignment.xml	Thu Apr 25 21:24:39 2024 +0000
@@ -0,0 +1,95 @@
+<?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 trim-alignment" id="qiime2__rescript__trim_alignment" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Trim alignment based on provided primers or specific positions.</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 trim_alignment '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="aligned_sequences" type="data" format="qza" label="aligned_sequences: FeatureData[AlignedSequence]" help="[required]  Aligned DNA sequences.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <conditional name="__q2galaxy__GUI__conditional__primer_fwd__" label="primer_fwd: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="primer_fwd: Str" help="[optional]  Forward primer used to find the start position for alignment trimming.">
+                    <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="primer_fwd" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="primer_fwd" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__primer_rev__" label="primer_rev: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="primer_rev: Str" help="[optional]  Reverse primer used to find the end position for alignment trimming.">
+                    <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="primer_rev" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="primer_rev" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+            <param name="position_start" type="integer" min="1" optional="true" label="position_start: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will begin. If not provided, alignment will notbe trimmed at the beginning. If forward primer isspecified this parameter will be ignored."/>
+            <param name="position_end" type="integer" min="1" optional="true" label="position_end: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will end. If not provided, alignment will not be trimmed at the end. If reverse primer is specified this parameter will be ignored."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript trim-alignment
+================================
+Trim alignment based on provided primers or specific positions.
+
+
+Outputs:
+--------
+:trimmed_sequences.qza: Trimmed sequence alignment.
+
+|  
+
+Description:
+------------
+Trim an existing alignment based on provided primers or specific, pre-defined positions. Primers take precedence over the positions,i.e. if both are provided, positions will be ignored.When using primers in combination with a DNA alignment, a new alignment will be generated to locate primer positions. Subsequently, start (5'-most) and end (3'-most) position from fwd and rev primer located within the new alignment is identified and used for slicing the original alignment.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 2eff5d70ecd5 test-data/.gitkeep