# HG changeset patch
# User q2d2
# Date 1714078571 0
# Node ID 05d47d652efbb47189dad18f0a21ce16fb6a5884

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 000000000000 -r 05d47d652efb qiime2__demux__tabulate_read_counts.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__demux__tabulate_read_counts.xml	Thu Apr 25 20:56:11 2024 +0000
@@ -0,0 +1,59 @@
+<?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: 2024.2.1)
+for:
+    qiime2 (version: 2024.2.0)
+-->
+<tool name="qiime2 demux tabulate-read-counts" id="qiime2__demux__tabulate_read_counts" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Tabulate counts per sample</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version demux</version_command>
+    <command detect_errors="exit_code">q2galaxy run demux tabulate_read_counts '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="sequences" type="data" format="qza" label="sequences: List[SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]]" help="[required]  One or more collections of demultiplexed sequences." multiple="true">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
+                <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="counts" format="qza" label="${tool.name} on ${on_string}: counts.qza" from_work_dir="counts.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: demux tabulate-read-counts
+===================================
+Tabulate counts per sample
+
+
+Outputs:
+--------
+:counts.qza: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Generate a per-sample count of sequence reads.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 05d47d652efb test-data/emp_single.test0.sample-metadata.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emp_single.test0.sample-metadata.tsv	Thu Apr 25 20:56:11 2024 +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
diff -r 000000000000 -r 05d47d652efb test-data/emp_single.test0.sequences.qza
Binary file test-data/emp_single.test0.sequences.qza has changed
diff -r 000000000000 -r 05d47d652efb test-data/summarize.test0.demux.qza
Binary file test-data/summarize.test0.demux.qza has changed