Mercurial > repos > q2d2 > qiime2__stats__mann_whitney_u_facet
changeset 0:3860c369685d 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 19:56:37 +0000 |
| parents | |
| children | |
| files | qiime2__stats__mann_whitney_u_facet.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, 162 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__stats__mann_whitney_u_facet.xml Wed Oct 30 19:56:37 2024 +0000 @@ -0,0 +1,112 @@ +<?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 mann-whitney-u-facet" id="qiime2__stats__mann_whitney_u_facet" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Per-facet Mann-Whitney U 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 mann_whitney_u_facet '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="staging_path_and_source_path"/> + </configfiles> + <inputs> + <param name="distribution" type="data" format="qza" label="distribution: Dist1D[Multi, Independent]¹ | Dist1D[NestedOrdered | NestedUnordered, Matched]² | Dist1D[NestedOrdered | NestedUnordered, Independent]³" help="[required]"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="Dist1D[Multi, Independent]"/> + <filter type="add_value" value="Dist1D[NestedOrdered | NestedUnordered, Matched]"/> + <filter type="add_value" value="Dist1D[NestedOrdered | NestedUnordered, Independent]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Dist1D[Multi, Independent]', 'Dist1D[NestedOrdered, Independent]', 'Dist1D[NestedOrdered, Matched]', 'Dist1D[NestedUnordered, Independent]', 'Dist1D[NestedUnordered, Matched]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="facet" type="select" label="facet: Str % Choices('within')¹'² | Str % Choices('within', 'across')³" help="[default: 'within'] Whether to facet within or across the outer group."> + <option value="within" selected="true">within (Str)</option> + <option value="across">across (Str)</option> + </param> + </section> + </inputs> + <outputs> + <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/> + </outputs> + <tests> + <test> + <param name="distribution" value="mann_whitney_u_facet.test0.dist.qza" ftype="qza"/> + <conditional name="__q2galaxy__GUI__conditional__facet__"> + <param name="__q2galaxy__GUI__select__" value="across"/> + <param name="facet" value="across"/> + </conditional> + <output name="stats" ftype="qza"/> + </test> + <test> + <param name="distribution" value="mann_whitney_u_facet.test1.dist.qza" ftype="qza"/> + <conditional name="__q2galaxy__GUI__conditional__facet__"> + <param name="__q2galaxy__GUI__select__" value="within"/> + <param name="facet" value="within"/> + </conditional> + <output name="stats" ftype="qza"/> + </test> + </tests> + <help> +QIIME 2: stats mann-whitney-u-facet +=================================== +Per-facet Mann-Whitney U Test + + +Outputs: +-------- +:stats.qza: <no description> + +| + +Description: +------------ + + +Examples: +--------- + +mann_whitney_u_facet_across +*************************** +Using the ``qiime2 stats mann-whitney-u-facet`` tool: + #. Set *"distribution"* to ``#: dist.qza`` + #. Expand the ``additional options`` section + + - Set *"facet"* to ``across`` + + #. Press the ``Execute`` button. + + +mann_whitney_u_facet_within +*************************** +Using the ``qiime2 stats mann-whitney-u-facet`` tool: + #. Set *"distribution"* to ``#: dist.qza`` + #. Expand the ``additional options`` section + + - Leave *"facet"* as its default value of ``within`` + + #. Press the ``Execute`` button. + + + +| + +</help> + <citations> + <citation type="doi">10.1214/aoms/1177730491</citation> + <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 19:56:37 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