Mercurial > repos > q2d2 > qiime2rescriptevaluate_taxonomy

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+++ b/qiime2__rescript__evaluate_taxonomy.xml	Thu Apr 25 21:22:52 2024 +0000
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+<?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 evaluate-taxonomy" id="qiime2__rescript__evaluate_taxonomy" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Compute summary statistics on taxonomy artifact(s).</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 evaluate_taxonomy '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="taxonomies" type="data" format="qza" label="taxonomies: List[FeatureData[Taxonomy]]" help="[required]  One or more taxonomies to evaluate." multiple="true">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Taxonomy]"/>
+            </options>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="labels" help="[optional]  List of labels to use for labeling evaluation results in the resulting visualization. Inputs are labeled with labels in the order that each is input. If there are fewer labels than inputs (or no labels), unnamed inputs are labeled numerically in sequential order. Extra labels are ignored." 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>
+            <conditional name="__q2galaxy__GUI__conditional__rank_handle_regex__" label="rank_handle_regex: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="rank_handle_regex: Str" help="[optional]  Regular expression indicating which taxonomic rank a label belongs to; this handle is stripped from the label prior to operating on the taxonomy. The net effect is that ambiguous or empty levels can be removed prior to comparison, enabling selection of taxonomies with more complete taxonomic information. For example, &quot;^[dkpcofgs]__&quot; will recognize greengenes or silva rank handles. ">
+                    <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="rank_handle_regex" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="rank_handle_regex" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="taxonomy_stats" format="qzv" label="${tool.name} on ${on_string}: taxonomy_stats.qzv" from_work_dir="taxonomy_stats.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript evaluate-taxonomy
+===================================
+Compute summary statistics on taxonomy artifact(s).
+
+
+Outputs:
+--------
+:taxonomy_stats.qzv: &lt;no description&gt;
+
+|
+
+Description:
+------------
+Compute summary statistics on taxonomy artifact(s) and visualize as interactive lineplots. Summary statistics include the number of unique labels, taxonomic entropy, and the number of features that are (un)classified at each taxonomic level. This action is useful for both reference taxonomies and classification results. The x-axis in these plots represents the taxonomic levels present in the input taxonomies so are labeled numerically instead of by rank, but typically for 7-level taxonomies these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class, 4 = order, 5 = family, 6 = genus, 7 = species.
+
+
+|
+
+</help>
+    <citations>
+        <citation type="doi">10.1128/mSystems.00219-18</citation>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>