Mercurial > repos > q2d2 > qiime2__stats__wilcoxon_srt
diff qiime2__stats__wilcoxon_srt.xml @ 0:3cbec5fc30ad draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
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| date | Wed, 30 Oct 2024 19:58:11 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__stats__wilcoxon_srt.xml Wed Oct 30 19:58:11 2024 +0000 @@ -0,0 +1,127 @@ +<?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: 2024.10.0) +for: + qiime2 (version: 2024.10.1) +--> +<tool name="qiime2 stats wilcoxon-srt" id="qiime2__stats__wilcoxon_srt" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Wilcoxon Signed Rank Test</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + </requirements> + <version_command>q2galaxy version stats</version_command> + <command detect_errors="exit_code">q2galaxy run stats wilcoxon_srt '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="distribution" type="data" format="qza" label="distribution: Dist1D[Ordered, Matched]" help="[required]"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="Dist1D[Ordered, Matched]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Ordered, Matched]']</validator> + </param> + <param name="compare" type="select" label="compare: Str % Choices('baseline', 'consecutive')" display="radio"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="baseline">baseline</option> + <option value="consecutive">consecutive</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="__q2galaxy__GUI__conditional__baseline_group__" label="baseline_group: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="baseline_group: Str" help="[optional] If "baseline" is the selected comparison, this is the column that will be used to compare all other groups against."> + <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="baseline_group" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="baseline_group" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <param name="alternative" type="select" label="alternative: Str % Choices('two-sided', 'greater', 'less')" display="radio"> + <option value="two-sided" selected="true">two-sided</option> + <option value="greater">greater</option> + <option value="less">less</option> + </param> + <param name="p_val_approx" type="select" label="p_val_approx: Str % Choices('auto', 'exact', 'asymptotic')" display="radio"> + <option value="auto" selected="true">auto</option> + <option value="exact">exact</option> + <option value="asymptotic">asymptotic</option> + </param> + <param name="ignore_empty_comparator" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_empty_comparator: Bool" help="[default: No] Ignore any group that does not have any overlapping subjects with comparison group. These groups will have NaNs in the stats table output"/> + </section> + </inputs> + <outputs> + <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> + </outputs> + <tests> + <test> + <param name="distribution" value="wilcoxon_srt.test0.timedist.qza" ftype="qza"/> + <param name="compare" value="baseline"/> + <param name="baseline_group" value="0"/> + <param name="p_val_approx" value="asymptotic"/> + <output name="stats" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: StatsTable\[Pairwise\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> + <help> +QIIME 2: stats wilcoxon-srt +=========================== +Wilcoxon Signed Rank Test + + +Outputs: +-------- +:stats.qza: The Wilcoxon SRT table for either the "baseline" or "consecutive" comparison. + +| + +Description: +------------ + + +Examples: +--------- + +wilcoxon_baseline0 +****************** +Using the ``qiime2 stats wilcoxon-srt`` tool: + #. Set *"distribution"* to ``#: timedist.qza`` + #. Set *"compare"* to ``baseline`` + #. Expand the ``additional options`` section + + #. Set *"baseline_group"* to ``0`` + #. Set *"p_val_approx"* to ``asymptotic`` + + #. Press the ``Execute`` button. + + + +| + +</help> + <citations> + <citation type="doi">https://doi.org/10.2307/3001968</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>