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Changeset 0:d6f4c80a29a2 (2024-10-30)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__stats commit 5f71b597c9495eae67a447744fded834f56ca1f7

added:
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

diff -r 000000000000 -r d6f4c80a29a2 qiime2__stats__alpha_group_significance.xml
--- /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

[

b'@@ -0,0 +1,268 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<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">\n+ <description>Alpha group significance test and plot</description>\n+ <xrefs>\n+ <xref type="bio.tools">qiime2</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/amplicon:2024.10</container>\n+ </requirements>\n+ <version_command>q2galaxy version stats</version_command>\n+ <command detect_errors="exit_code">q2galaxy run stats alpha_group_significance \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="staging_path_and_source_path"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="alpha_diversity" type="data" format="qza" label="alpha_diversity: SampleData[AlphaDiversity]" help="[required] Alpha diversity which will become the "measure"">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="SampleData[AlphaDiversity]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'SampleData[AlphaDiversity]\']</validator>\n+ </param>\n+ <repeat name="metadata" min="1" help="[required] Sample metadata to use" title="metadata: Metadata">\n+ <conditional name="__q2galaxy__GUI__conditional__metadata__">\n+ <param name="type" type="select" label="metadata: Metadata">\n+ <option value="tsv" selected="true">Metadata from TSV</option>\n+ <option value="qza">Metadata from Artifact</option>\n+ </param>\n+ <when value="tsv">\n+ <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>\n+ </when>\n+ <when value="qza">\n+ <param name="source" type="data" format="qza" label="Metadata Source"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ <repeat name="columns" min="1" help="[required] Columns to include as group information" title="columns: List[Str]">\n+ <param name="element" type="text" label="element: Str" help="[required]">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <conditional name="__q2galaxy__GUI__conditional__subject__">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="subject: Str % Choices(\'\')\xc2\xb9\'\xc2\xb3 | Str\xc2\xb2\'\xe2\x81\xb4" help="[default: \'\'] If provided, will cause the results to be matched for repeated measures.">\n+ <option value="" selected="true"> (Str)</option>\n+ <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>\n+ <option value="__q2galaxy__::control::Str" selected="true">Provide a value (Str)</option>\n+ </param>\n+ <when value="">\n+ <param name="subject" type="hidden" value=""/>\n+ </when>\n+ <when value="__q2galaxy__::control::Str">\n+ <param name="subject" type="text" value="" label="subject: Str" help="[default: \'\'] If provided, will cause'..b'a.tsv" ftype="qiime2.tabular"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="columns">\n+ <param name="element" value="genotype"/>\n+ </repeat>\n+ <repeat name="columns">\n+ <param name="element" value="donor_status"/>\n+ </repeat>\n+ <output name="distribution" ftype="qza">\n+ <assert_contents>\n+ <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">\n+ <has_line_matching expression="type: Dist1D\\[Multi,\\ Independent\\]"/>\n+ </has_archive_member>\n+ </assert_contents>\n+ </output>\n+ <output name="stats" ftype="qza"/>\n+ <output name="raincloud" ftype="qzv"/>\n+ </test>\n+ </tests>\n+ <help>\n+QIIME 2: stats alpha-group-significance\n+=======================================\n+Alpha group significance test and plot\n+\n+\n+Outputs:\n+--------\n+:distribution.qza: Dist1D generated by metadata and alpha diversity.\n+:stats.qza: A stats table of the per-group/timepoint results\n+:raincloud.qzv: A visualization of the distribution and statistics\n+\n+| \n+\n+Description:\n+------------\n+Will select between Wilcoxon SRT and Mann-Whitney U depending on the presence of repeated measures.\n+\n+Examples:\n+---------\n+\n+alpha_group_significance_faith_pd\n+*********************************\n+Using the ``qiime2 stats alpha-group-significance`` tool:\n+ #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza``\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. For *"columns"*, use the ``+ columns`` button to add the corresponding values:\n+\n+ #. Add *"element"* set to ``genotype``\n+ #. Add *"element"* set to ``donor_status``\n+\n+ #. Expand the ``additional options`` section\n+\n+ #. Set *"subject"* to ``mouse_id``\n+ #. Set *"timepoint"* to ``days_post_transplant``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza``\n+ - ``dist.qza``\n+ * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza``\n+ - ``stats.qza``\n+ * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv``\n+ - ``raincloud.qzv``\n+\n+Using the ``qiime2 stats alpha-group-significance`` tool:\n+ #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza``\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. For *"columns"*, use the ``+ columns`` button to add the corresponding values:\n+\n+ #. Add *"element"* set to ``genotype``\n+ #. Add *"element"* set to ``donor_status``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 stats alpha-group-significance [...] : distribution.qza``\n+ - ``dist2.qza``\n+ * - ``#: qiime2 stats alpha-group-significance [...] : stats.qza``\n+ - ``stats2.qza``\n+ * - ``#: qiime2 stats alpha-group-significance [...] : raincloud.qzv``\n+ - ``raincloud2.qzv``\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'

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diff -r 000000000000 -r d6f4c80a29a2 test-data/alpha_group_significance.test0.metadata.tsv
--- /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

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