Mercurial > repos > q2d2 > qiime2__stats__alpha_group_significance
changeset 0:d6f4c80a29a2 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 19:56:51 +0000 |
| parents | |
| children | |
| files | qiime2__stats__alpha_group_significance.xml test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza test-data/alpha_group_significance.test0.metadata.tsv test-data/mann_whitney_u.test0.refdist.qza test-data/mann_whitney_u.test0.timedist.qza test-data/mann_whitney_u_facet.test0.dist.qza test-data/mann_whitney_u_facet.test1.dist.qza test-data/plot_rainclouds.test0.dist.qza test-data/wilcoxon_srt.test0.timedist.qza test-data/wilcoxon_srt_facet.test0.dist.qza |
| diffstat | 10 files changed, 318 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__stats__alpha_group_significance.xml Wed Oct 30 19:56:51 2024 +0000 @@ -0,0 +1,268 @@ +<?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 alpha-group-significance" id="qiime2__stats__alpha_group_significance" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Alpha group significance test and plot</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 alpha_group_significance '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required] Alpha diversity which will become the "measure""> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[AlphaDiversity]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[AlphaDiversity]']</validator> + </param> + <repeat name="metadata" min="1" help="[required] Sample metadata to use" title="metadata: Metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" type="select" label="metadata: Metadata"> + <option value="tsv" selected="true">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + </when> + </conditional> + </repeat> + <repeat name="columns" min="1" help="[required] Columns to include as group information" title="columns: 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) > 0</validator> + </param> + </repeat> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="__q2galaxy__GUI__conditional__subject__"> + <param name="__q2galaxy__GUI__select__" type="select" label="subject: Str % Choices('')¹'³ | Str²'⁴" help="[default: ''] If provided, will cause the results to be matched for repeated measures."> + <option value="" selected="true"> (Str)</option> + <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option> + <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option> + </param> + <when value=""> + <param name="subject" type="hidden" value=""/> + </when> + <when value="__q2galaxy__::control::Str"> + <param name="subject" type="text" value="" label="subject: Str" help="[default: ''] If provided, will cause the results to be matched for repeated measures."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + <when value="__q2galaxy__::control::Str"> + <param name="subject" type="text" value="" label="subject: Str" help="[default: ''] If provided, will cause the results to be matched for repeated measures."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__timepoint__"> + <param name="__q2galaxy__GUI__select__" type="select" label="timepoint: Str % Choices('')¹'² | Str³'⁴" help="[default: ''] If provided, will cause the results to be stratified by timepoint. Required if using ``subject``."> + <option value="" selected="true"> (Str)</option> + <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option> + <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option> + </param> + <when value=""> + <param name="timepoint" type="hidden" value=""/> + </when> + <when value="__q2galaxy__::control::Str"> + <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: ''] If provided, will cause the results to be stratified by timepoint. Required if using ``subject``."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + <when value="__q2galaxy__::control::Str"> + <param name="timepoint" type="text" value="" label="timepoint: Str" help="[default: ''] If provided, will cause the results to be stratified by timepoint. Required if using ``subject``."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + </section> + </inputs> + <outputs> + <data name="distribution" format="qza" label="${tool.name} on ${on_string}: distribution.qza" from_work_dir="distribution.qza"/> + <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> + <data name="raincloud" format="qzv" label="${tool.name} on ${on_string}: raincloud.qzv" from_work_dir="raincloud.qzv"/> + </outputs> + <tests> + <test> + <param name="alpha_diversity" value="alpha_group_significance.test0.alpha-div-faith-pd.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="alpha_group_significance.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <repeat name="columns"> + <param name="element" value="genotype"/> + </repeat> + <repeat name="columns"> + <param name="element" value="donor_status"/> + </repeat> + <conditional name="__q2galaxy__GUI__conditional__subject__"> + <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Str"/> + <param name="subject" value="mouse_id"/> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__timepoint__"> + <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Str"/> + <param name="timepoint" value="days_post_transplant"/> + </conditional> + <output name="distribution" 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: Dist1D\[NestedOrdered,\ Matched\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="stats" ftype="qza"/> + <output name="raincloud" ftype="qzv"/> + <param name="alpha_diversity" value="alpha_group_significance.test0.alpha-div-faith-pd.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="alpha_group_significance.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <repeat name="columns"> + <param name="element" value="genotype"/> + </repeat> + <repeat name="columns"> + <param name="element" value="donor_status"/> + </repeat> + <output name="distribution" 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: Dist1D\[Multi,\ Independent\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="stats" ftype="qza"/> + <output name="raincloud" ftype="qzv"/> + </test> + </tests> + <help> +QIIME 2: stats alpha-group-significance +======================================= +Alpha group significance test and plot + + +Outputs: +-------- +:distribution.qza: Dist1D generated by metadata and alpha diversity. +:stats.qza: A stats table of the per-group/timepoint results +:raincloud.qzv: A visualization of the distribution and statistics + +| + +Description: +------------ +Will select between Wilcoxon SRT and Mann-Whitney U depending on the presence of repeated measures. + +Examples: +--------- + +alpha_group_significance_faith_pd +********************************* +Using the ``qiime2 stats alpha-group-significance`` tool: + #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. For *"columns"*, use the ``+ columns`` button to add the corresponding values: + + #. Add *"element"* set to ``genotype`` + #. Add *"element"* set to ``donor_status`` + + #. Expand the ``additional options`` section + + #. Set *"subject"* to ``mouse_id`` + #. Set *"timepoint"* to ``days_post_transplant`` + + #. Press the ``Execute`` button. + +Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza`` + - ``dist.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza`` + - ``stats.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv`` + - ``raincloud.qzv`` + +Using the ``qiime2 stats alpha-group-significance`` tool: + #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. For *"columns"*, use the ``+ columns`` button to add the corresponding values: + + #. Add *"element"* set to ``genotype`` + #. Add *"element"* set to ``donor_status`` + + #. Press the ``Execute`` button. + +Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza`` + - ``dist2.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza`` + - ``stats2.qza`` + * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv`` + - ``raincloud2.qzv`` + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alpha_group_significance.test0.metadata.tsv Wed Oct 30 19:56:51 2024 +0000 @@ -0,0 +1,50 @@ +sample_name barcode mouse_id genotype cage_id donor donor_status days_post_transplant genotype_and_donor_status +#q2:types categorical categorical categorical categorical categorical categorical numeric categorical +recip.220.WT.OB1.D7 CCTCCGTCATGG 457 wild type C35 hc_1 Healthy 49 wild type and Healthy +recip.290.ASO.OB2.D1 AACAGTAAACAA 456 susceptible C35 hc_1 Healthy 49 susceptible and Healthy +recip.389.WT.HC2.D21 ATGTATCAATTA 435 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D14 GTCAGTATGGCT 435 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.391.ASO.PD2.D21 AGACAGTAGGAG 437 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D7 GGTCTTAGCACC 435 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.400.ASO.HC2.D14 CGTTCGCTAGCC 437 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.401.ASO.HC2.D7 ATTTACAATTGA 437 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.403.ASO.PD2.D21 CGCAGATTAGTA 456 susceptible C35 hc_1 Healthy 21 susceptible and Healthy +recip.411.ASO.HC2.D14 ATGTTAGGGAAT 456 susceptible C35 hc_1 Healthy 14 susceptible and Healthy +recip.411.ASO.HC2.D21 CTCATATGCTAT 457 wild type C35 hc_1 Healthy 21 wild type and Healthy +recip.411.ASO.HC2.D49 GCAACGAACGAG 435 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.412.ASO.HC2.D14 AAGTGGCTATCC 457 wild type C35 hc_1 Healthy 14 wild type and Healthy +recip.412.ASO.HC2.D7 GCATTCGGCGTT 456 susceptible C35 hc_1 Healthy 7 susceptible and Healthy +recip.413.WT.HC2.D7 ACCAGTGACTCA 457 wild type C35 hc_1 Healthy 7 wild type and Healthy +recip.456.ASO.HC3.D49 ACGGCGTTATGT 468 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.458.ASO.HC3.D21 ACGGCCCTGGAG 468 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.458.ASO.HC3.D49 CATTTGACGACG 469 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.459.WT.HC3.D14 ACATGGGCGGAA 468 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.459.WT.HC3.D21 CATAAATTCTTG 469 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.459.WT.HC3.D49 GCTGCGTATACC 536 susceptible C43 pd_1 PD 49 susceptible and PD +recip.460.WT.HC3.D14 CTGCGGATATAC 469 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.460.WT.HC3.D21 GTCAATTAGTGG 536 susceptible C43 pd_1 PD 21 susceptible and PD +recip.460.WT.HC3.D49 GAGAAGCTTATA 537 wild type C43 pd_1 PD 49 wild type and PD +recip.460.WT.HC3.D7 GACCCGTTTCGC 468 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.461.ASO.HC3.D21 AGCCCGCAAAGG 537 wild type C43 pd_1 PD 21 wild type and PD +recip.461.ASO.HC3.D49 GGCGTAACGGCA 538 wild type C44 pd_1 PD 49 wild type and PD +recip.461.ASO.HC3.D7 ATTGCCTTGATT 469 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.462.WT.PD3.D14 GTGAGGGCAAGT 536 susceptible C43 pd_1 PD 14 susceptible and PD +recip.462.WT.PD3.D21 GGCCTATAAGTC 538 wild type C44 pd_1 PD 21 wild type and PD +recip.462.WT.PD3.D49 AATACAGACCTG 539 susceptible C44 pd_1 PD 49 susceptible and PD +recip.462.WT.PD3.D7 TTAGGATTCTAT 536 susceptible C43 pd_1 PD 7 susceptible and PD +recip.463.WT.PD3.D14 ATATTGGCAGCC 537 wild type C43 pd_1 PD 14 wild type and PD +recip.463.WT.PD3.D21 CGCGGCGCAGCT 539 susceptible C44 pd_1 PD 21 susceptible and PD +recip.463.WT.PD3.D7 GTTTATCTTAAG 537 wild type C43 pd_1 PD 7 wild type and PD +recip.464.WT.PD3.D14 TCATCCGTCGGC 538 wild type C44 pd_1 PD 14 wild type and PD +recip.465.ASO.PD3.D14 GGCTTCGGAGCG 539 susceptible C44 pd_1 PD 14 susceptible and PD +recip.465.ASO.PD3.D7 CAGTCTAGTACG 538 wild type C44 pd_1 PD 7 wild type and PD +recip.466.ASO.PD3.D7 GTGGGACTGCGC 539 susceptible C44 pd_1 PD 7 susceptible and PD +recip.467.WT.HC3.D49.a GTCAGGTGCGGC 437 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.467.WT.HC3.D49.b GTTAACTTACTA 546 susceptible C49 pd_1 PD 49 susceptible and PD +recip.536.ASO.PD4.D49 CAAATTCGGGAT 547 wild type C49 pd_1 PD 49 wild type and PD +recip.537.WT.PD4.D21 CTCTATTCCACC 546 susceptible C49 pd_1 PD 21 susceptible and PD +recip.538.WT.PD4.D21 ATGGATAGCTAA 547 wild type C49 pd_1 PD 21 wild type and PD +recip.539.ASO.PD4.D14 GATCCGGCAGGA 546 susceptible C49 pd_1 PD 14 susceptible and PD +recip.539.ASO.PD4.D7 GTTCGAGTGAAT 546 susceptible C49 pd_1 PD 7 susceptible and PD +recip.540.ASO.HC4.D14 CTTCCAACTCAT 547 wild type C49 pd_1 PD 14 wild type and PD +recip.540.ASO.HC4.D7 CGGCCTAAGTTC 547 wild type C49 pd_1 PD 7 wild type and PD