Mercurial > repos > q2d2 > qiime2__stats__collate_stats

changeset 0:10e19418eedb draft default tip

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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 19:58:26 +0000
parents
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files qiime2__stats__collate_stats.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, 110 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__stats__collate_stats.xml	Wed Oct 30 19:58:26 2024 +0000
@@ -0,0 +1,60 @@
+<?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 collate-stats" id="qiime2__stats__collate_stats" version="0+unknown-q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Combine and FDR correct multiple stats</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 collate_stats '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="tables" type="data" format="qza" label="tables: Collection[StatsTable[Pairwise]]" help="[required]" multiple="true">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="StatsTable[Pairwise]"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: stats collate-stats
+============================
+Combine and FDR correct multiple stats
+
+
+Outputs:
+--------
+:table.qza: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Converts a collection of stats tables into a single table
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
Binary file test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alpha_group_significance.test0.metadata.tsv	Wed Oct 30 19:58:26 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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