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changeset 0:6afd848c3650 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 21:20:53 +0000
parents
children 3fdb4839347a
files qiime2__rescript__evaluate_cross_validate.xml test-data/.gitkeep
diffstat 1 files changed, 98 insertions(+), 0 deletions(-) [+]
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+++ b/qiime2__rescript__evaluate_cross_validate.xml	Thu Apr 25 21:20:53 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-cross-validate" id="qiime2__rescript__evaluate_cross_validate" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Evaluate DNA sequence reference database via cross-validated taxonomic classification.</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_cross_validate '$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]  Reference sequences to use for classifier training/testing.">
+            <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]  Reference taxonomy to use for classifier training/testing.">
+            <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">
+            <param name="k" type="integer" min="2" value="3" label="k: Int % Range(2, None)" help="[default: 3]  Number of stratified folds."/>
+            <param name="random_state" type="integer" min="0" value="0" label="random_state: Int % Range(0, None)" help="[default: 0]  Seed used by the random number generator."/>
+            <conditional name="__q2galaxy__GUI__conditional__reads_per_batch__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="reads_per_batch: Int % Range(1, None) | Str % Choices('auto')" help="[default: 'auto']  Number of reads to process in each batch. If &quot;auto&quot;, this parameter is autoscaled to min( number of query sequences / n_jobs, 20000).">
+                    <option value="auto" selected="true">auto (Str)</option>
+                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option>
+                </param>
+                <when value="auto">
+                    <param name="reads_per_batch" type="hidden" value="auto"/>
+                </when>
+                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
+                    <param name="reads_per_batch" type="integer" min="1" value="" label="reads_per_batch: Int % Range(1, None)" help="[required]  Number of reads to process in each batch. If &quot;auto&quot;, this parameter is autoscaled to min( number of query sequences / n_jobs, 20000)."/>
+                </when>
+            </conditional>
+            <conditional name="__q2galaxy__GUI__conditional__confidence__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="confidence: Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable')" help="[default: 0.7]  Confidence threshold for limiting taxonomic depth. Set to &quot;disable&quot; to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.">
+                    <option value="disable">disable (Str)</option>
+                    <option value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)" selected="true">Provide a value (Float % Range(0, 1, inclusive_end=True))</option>
+                </param>
+                <when value="disable">
+                    <param name="confidence" type="hidden" value="disable"/>
+                </when>
+                <when value="__q2galaxy__::control::Float X Range(0__comma__ 1__comma__ inclusive_end=True)">
+                    <param name="confidence" type="float" min="0" max="1" value="0.7" label="confidence: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.7]  Confidence threshold for limiting taxonomic depth. Set to &quot;disable&quot; to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments."/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="expected_taxonomy" format="qza" label="${tool.name} on ${on_string}: expected_taxonomy.qza" from_work_dir="expected_taxonomy.qza"/>
+        <data name="observed_taxonomy" format="qza" label="${tool.name} on ${on_string}: observed_taxonomy.qza" from_work_dir="observed_taxonomy.qza"/>
+        <data name="evaluation" format="qzv" label="${tool.name} on ${on_string}: evaluation.qzv" from_work_dir="evaluation.qzv"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: rescript evaluate-cross-validate
+=========================================
+Evaluate DNA sequence reference database via cross-validated taxonomic classification.
+
+
+Outputs:
+--------
+:expected_taxonomy.qza: Expected taxonomic label for each input sequence. Taxonomic labels may be truncated due to k-fold CV and stratification.
+:observed_taxonomy.qza: Observed taxonomic label for each input sequence, predicted by cross-validation.
+:evaluation.qzv: Visualization of cross-validated accuracy results.
+
+|  
+
+Description:
+------------
+Evaluate DNA sequence reference database via cross-validated taxonomic classification. Unique taxonomic labels are truncated to enable appropriate label stratification. See the cited reference (Bokulich et al. 2018) for more details.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1186/s40168-018-0470-z</citation>
+        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>