# HG changeset patch
# User q2d2
# Date 1714080203 0
# Node ID f4ea39668a42b1a5252f46b7183adb51f013ab6d

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

diff -r 000000000000 -r f4ea39668a42 qiime2__rescript__edit_taxonomy.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__rescript__edit_taxonomy.xml	Thu Apr 25 21:23:23 2024 +0000
@@ -0,0 +1,98 @@
+<?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 edit-taxonomy" id="qiime2__rescript__edit_taxonomy" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Edit taxonomy strings with find and replace terms.</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 edit_taxonomy '$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 strings data to be edited.">
+            <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">
+            <conditional name="replacement_map">
+                <param name="type" type="select" label="replacement_map: MetadataColumn[Categorical]" help="[optional]  A tab-delimitad metadata file in which the strings in the 'id' column are replaced by the 'replacement-strings' in the second column. All strings in the 'id' column must be unique!">
+                    <option value="none" selected="true">None (default)</option>
+                    <option value="tsv">Metadata from TSV</option>
+                    <option value="qza">Metadata from Artifact</option>
+                </param>
+                <when value="none"/>
+                <when value="tsv">
+                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                    <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
+                        <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
+                    </param>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                    <param name="column" type="text" label="Column Name">
+                        <validator type="empty_field"/>
+                    </param>
+                </when>
+            </conditional>
+            <repeat name="search_strings" help="[optional]  Only used in conjuntion with 'replacement-strings'. Each string in this list is searched for and replaced with a string in the list of 'replace-ment-strings'. That is the first string in 'search-strings' is  replaced with the first string in 'replacement-strings', and so on. The number of 'search-strings' must be equal to the number of replacement strings." title="search_strings: 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="replacement_strings" help="[optional]  Only used in conjuntion with 'search-strings'. This must contain the same number of replacement strings as search strings. See 'search-strings' parameter text for more details." title="replacement_strings: 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>
+            <param name="use_regex" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="use_regex: Bool" help="[default: No]  Toggle regular expressions. By default, only litereal substring matching is performed."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="edited_taxonomy" format="qza" label="${tool.name} on ${on_string}: edited_taxonomy.qza" from_work_dir="edited_taxonomy.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript edit-taxonomy
+===============================
+Edit taxonomy strings with find and replace terms.
+
+
+Outputs:
+--------
+:edited_taxonomy.qza: Taxonomy in which the original strings are replaced by user-supplied strings.
+
+|  
+
+Description:
+------------
+A method that allows the user to edit taxonomy strings. This is often used to fix inconsistent and/or inccorect taxonomic annotations. The user can either provide two separate lists of strings, i.e. 'search-strings', and 'replacement-strings', on the command line, and/or a single tab-delimited replacement map file containing a list of these strings. In both cases the number of search strings must match the number of replacement strings. That is the first string in 'search-strings' is replaced with the first string in 'replacement-strings', and so on. In the case that both search / replacement strings, and a replacement map file are provided, they will be merged.
+
+
+|  
+
+</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 f4ea39668a42 test-data/.gitkeep