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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 18:54:07 +0000
parents
children
files qiime2__feature_table__normalize.xml test-data/filter_features.test0.feature-table.qza test-data/filter_features_conditionally.test0.feature-table.qza test-data/filter_samples.test0.feature-table.qza test-data/filter_samples.test0.sample-metadata.tsv test-data/filter_samples.test1.feature-table.qza test-data/filter_samples.test1.sample-metadata.tsv test-data/filter_samples.test2.feature-table.qza test-data/filter_samples.test2.sample-metadata.tsv test-data/filter_samples.test3.feature-table.qza test-data/filter_samples.test3.sample-metadata.tsv test-data/filter_samples.test4.feature-table.qza test-data/filter_samples.test4.sample-metadata.tsv test-data/filter_samples.test5.feature-table.qza test-data/filter_samples.test6.feature-table.qza test-data/group.test0.feature-table.qza test-data/group.test0.sample-metadata.tsv test-data/merge.test0.feature-table1.qza test-data/merge.test0.feature-table2.qza test-data/merge.test1.feature-table1.qza test-data/merge.test1.feature-table2.qza test-data/merge.test1.feature-table3.qza test-data/merge_seqs.test0.seqs1.qza test-data/merge_seqs.test0.seqs2.qza test-data/merge_taxa.test0.tax1.qza test-data/merge_taxa.test0.tax2.qza test-data/summarize.test0.feature-table.qza test-data/summarize_plus.test0.feature-table.qza test-data/tabulate_feature_frequencies.test0.feature-table.qza test-data/tabulate_sample_frequencies.test0.feature-table.qza test-data/tabulate_seqs.test0.rep-seqs.qza test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza test-data/tabulate_seqs.test1.single-taxonomy.qza test-data/tabulate_seqs.test2.multi-taxonomy/.order test-data/tabulate_seqs.test2.multi-taxonomy/GG1.qza test-data/tabulate_seqs.test2.multi-taxonomy/GG2.qza test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza
diffstat 37 files changed, 309 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__feature_table__normalize.xml	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,91 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2025, 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: 2025.4.0)
+for:
+    qiime2 (version: 2025.4.0)
+-->
+<tool name="qiime2 feature-table normalize" id="qiime2__feature_table__normalize" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
+    <description>Normalize FeatureTable</description>
+    <xrefs>
+        <xref type="bio.tools">qiime2</xref>
+    </xrefs>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="exit_code">q2galaxy run feature_table normalize '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  Feature table with gene counts.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator>
+        </param>
+        <param name="method" type="select" label="method: Str % Choices('tpm')¹ | Str % Choices('fpkm')² | Str % Choices('tmm')³ | Str % Choices('uq')⁴ | Str % Choices('cuf')⁵ | Str % Choices('ctf')⁶ | Str % Choices('cpm')⁷" help="[required]  Specify the normalization method to be used. Use FPKM or TPM for within comparisons and TMM, UQ, CUF or CTF for between sample camparisons. Check https://www.genialis.com/wp-content/uploads/2023/12/2023-Normalizing-RNA-seq-data-in-Python-with-RNAnorm.pdf for more information on the methods.">
+            <option value="__q2galaxy__::literal::None" selected="true">Selection required</option>
+            <option value="tpm">tpm (Str)</option>
+            <option value="fpkm">fpkm (Str)</option>
+            <option value="tmm">tmm (Str)</option>
+            <option value="uq">uq (Str)</option>
+            <option value="cuf">cuf (Str)</option>
+            <option value="ctf">ctf (Str)</option>
+            <option value="cpm">cpm (Str)</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">
+            <param name="gene_length" type="data" format="qza" optional="true" label="gene_length: FeatureData[SequenceCharacteristics % Properties('length')]" help="[optional]  Gene lengths of all genes in the feature table.">
+                <options options_filter_attribute="metadata.semantic_type">
+                    <filter type="add_value" value="FeatureData[SequenceCharacteristics % Properties('length')]"/>
+                </options>
+                <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["FeatureData[SequenceCharacteristics % Properties('length')]"]</validator>
+            </param>
+            <param name="m_trim" type="float" min="0" max="1" optional="true" label="m_trim: Float % Range(0, 1, inclusive_end=True)" help="[optional]  Two sided cutoff for M-values. Can only be used for methods TMM and CTF. (default = 0.3)"/>
+            <param name="a_trim" type="float" min="0" max="1" optional="true" label="a_trim: Float % Range(0, 1, inclusive_end=True)" help="[optional]  Two sided cutoff for A-values. Can only be used for methods TMM and CTF. (default = 0.05)"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="normalized_table" format="qza" label="${tool.name} on ${on_string}: normalized_table.qza" from_work_dir="normalized_table.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: feature-table normalize
+================================
+Normalize FeatureTable
+
+
+Outputs:
+--------
+:normalized_table.qza: Feature table normalized with specified method.
+
+|  
+
+Description:
+------------
+Normalize FeatureTable by gene length, library size and composition with common methods for RNA-seq.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="bibtex">@misc{cite1,
+ author = {Zmrzlikar, Jure and Žganec, Matjaž and Ausec, Luka and Štajdohar, Miha},
+ month = {July},
+ title = {RNAnorm: RNA-seq data normalization in Python},
+ url = {https://github.com/genialis/RNAnorm},
+ version = {2.1.0},
+ year = {2023}
+}
+</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
Binary file test-data/filter_features.test0.feature-table.qza has changed
Binary file test-data/filter_features_conditionally.test0.feature-table.qza has changed
Binary file test-data/filter_samples.test0.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test0.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
Binary file test-data/filter_samples.test1.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test1.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
Binary file test-data/filter_samples.test2.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test2.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
Binary file test-data/filter_samples.test3.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test3.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
Binary file test-data/filter_samples.test4.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filter_samples.test4.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
Binary file test-data/filter_samples.test5.feature-table.qza has changed
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Binary file test-data/group.test0.feature-table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/group.test0.sample-metadata.tsv	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,36 @@
+sample-id	barcode-sequence	body-site	year	month	day	subject	reported-antibiotic-usage	days-since-experiment-start
+#q2:types	categorical	categorical	numeric	numeric	numeric	categorical	categorical	numeric
+L1S8	AGCTGACTAGTC	gut	2008	10	28	subject-1	Yes	0
+L1S57	ACACACTATGGC	gut	2009	1	20	subject-1	No	84
+L1S76	ACTACGTGTGGT	gut	2009	2	17	subject-1	No	112
+L1S105	AGTGCGATGCGT	gut	2009	3	17	subject-1	No	140
+L2S155	ACGATGCGACCA	left palm	2009	1	20	subject-1	No	84
+L2S175	AGCTATCCACGA	left palm	2009	2	17	subject-1	No	112
+L2S204	ATGCAGCTCAGT	left palm	2009	3	17	subject-1	No	140
+L2S222	CACGTGACATGT	left palm	2009	4	14	subject-1	No	168
+L3S242	ACAGTTGCGCGA	right palm	2008	10	28	subject-1	Yes	0
+L3S294	CACGACAGGCTA	right palm	2009	1	20	subject-1	No	84
+L3S313	AGTGTCACGGTG	right palm	2009	2	17	subject-1	No	112
+L3S341	CAAGTGAGAGAG	right palm	2009	3	17	subject-1	No	140
+L3S360	CATCGTATCAAC	right palm	2009	4	14	subject-1	No	168
+L5S104	CAGTGTCAGGAC	tongue	2008	10	28	subject-1	Yes	0
+L5S155	ATCTTAGACTGC	tongue	2009	1	20	subject-1	No	84
+L5S174	CAGACATTGCGT	tongue	2009	2	17	subject-1	No	112
+L5S203	CGATGCACCAGA	tongue	2009	3	17	subject-1	No	140
+L5S222	CTAGAGACTCTT	tongue	2009	4	14	subject-1	No	168
+L1S140	ATGGCAGCTCTA	gut	2008	10	28	subject-2	Yes	0
+L1S208	CTGAGATACGCG	gut	2009	1	20	subject-2	No	84
+L1S257	CCGACTGAGATG	gut	2009	3	17	subject-2	No	140
+L1S281	CCTCTCGTGATC	gut	2009	4	14	subject-2	No	168
+L2S240	CATATCGCAGTT	left palm	2008	10	28	subject-2	Yes	0
+L2S309	CGTGCATTATCA	left palm	2009	1	20	subject-2	No	84
+L2S357	CTAACGCAGTCA	left palm	2009	3	17	subject-2	No	140
+L2S382	CTCAATGACTCA	left palm	2009	4	14	subject-2	No	168
+L3S378	ATCGATCTGTGG	right palm	2008	10	28	subject-2	Yes	0
+L4S63	CTCGTGGAGTAG	right palm	2009	1	20	subject-2	No	84
+L4S112	GCGTTACACACA	right palm	2009	3	17	subject-2	No	140
+L4S137	GAACTGTATCTC	right palm	2009	4	14	subject-2	No	168
+L5S240	CTGGACTCATAG	tongue	2008	10	28	subject-2	Yes	0
+L6S20	GAGGCTCATCAT	tongue	2009	1	20	subject-2	No	84
+L6S68	GATACGTCCTGA	tongue	2009	3	17	subject-2	No	140
+L6S93	GATTAGCACTCT	tongue	2009	4	14	subject-2	No	168
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Binary file test-data/tabulate_seqs.test1.single-taxonomy.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabulate_seqs.test2.multi-taxonomy/.order	Mon May 05 18:54:07 2025 +0000
@@ -0,0 +1,2 @@
+GG1
+GG2
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