Mercurial > repos > q2d2 > qiime2__demux__emp_single

changeset 1:335abb486193 draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author q2d2
date Fri, 13 Jan 2023 22:43:21 +0000
parents 320c9af45b63
children 75b07a996ac0
files qiime2__demux__emp_single.xml test-data/.gitkeep test-data/emp_single.test0.sample-metadata.tsv test-data/emp_single.test0.sequences.qza test-data/summarize.test0.demux.qza
diffstat 4 files changed, 95 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__demux__emp_single.xml	Mon Aug 29 19:27:37 2022 +0000
+++ b/qiime2__demux__emp_single.xml	Fri Jan 13 22:43:21 2023 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2022, QIIME 2 development team.
+Copyright (c) 2023, 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: 2022.8.1)
+    q2galaxy (version: 2022.11.1)
 for:
-    qiime2 (version: 2022.8.1)
+    qiime2 (version: 2022.11.1)
 -->
-<tool name="qiime2 demux emp-single" id="qiime2__demux__emp_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 demux emp-single" id="qiime2__demux__emp_single" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
     <description>Demultiplex sequence data generated with the EMP protocol.</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2022.8</container>
+        <container type="docker">quay.io/qiime2/core:2022.11</container>
     </requirements>
     <version_command>q2galaxy version demux</version_command>
-    <command detect_errors="aggressive">q2galaxy run demux emp_single '$inputs'</command>
+    <command detect_errors="exit_code">q2galaxy run demux emp_single '$inputs'</command>
     <configfiles>
         <inputs name="inputs" data_style="paths"/>
     </configfiles>
@@ -58,7 +58,30 @@
         <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
         <data name="error_correction_details" format="qza" label="${tool.name} on ${on_string}: error_correction_details.qza" from_work_dir="error_correction_details.qza"/>
     </outputs>
-    <tests/>
+    <tests>
+        <test>
+            <param name="seqs" value="emp_single.test0.sequences.qza" ftype="qza"/>
+            <conditional name="barcodes">
+                <param name="type" value="tsv"/>
+                <param name="source" value="emp_single.test0.sample-metadata.tsv" ftype="qiime2.tabular"/>
+                <param name="column" value="2"/>
+            </conditional>
+            <output name="per_sample_sequences" ftype="qza">
+                <assert_contents>
+                    <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">
+                        <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+            <output name="error_correction_details" ftype="qza">
+                <assert_contents>
+                    <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">
+                        <has_line_matching expression="type: ErrorCorrectionDetails"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
     <help>
 QIIME 2: demux emp-single
 =========================
@@ -76,6 +99,35 @@
 ------------
 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data generated with the Earth Microbiome Project (EMP) amplicon sequencing protocol. Details about this protocol can be found at http://www.earthmicrobiome.org/protocols-and-standards/
 
+Examples:
+---------
+
+demux
+*****
+Using the ``qiime2 demux emp-single`` tool:
+ #. Set *"seqs"* to ``#: sequences.qza``
+ #. For *"barcodes"*:
+
+    #. Leave as ``Metadata from TSV``
+    #. Set *"Metadata Source"* to ``sample-metadata.tsv``
+    #. Set *"Column Name"* to ``barcode-sequence``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
+ (Renaming is optional, but it will make any subsequent steps easier to complete.)
+
+ .. list-table::
+    :align: left
+    :header-rows: 1
+
+    * - History Name
+      - *"Name"* to set (be sure to press ``Save``)
+    * - ``#: qiime2 demux emp-single [...] : per_sample_sequences.qza``
+      - ``demux.qza``
+    * - ``#: qiime2 demux emp-single [...] : error_correction_details.qza``
+      - ``demux-details.qza``
+
 
 |  
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/emp_single.test0.sample-metadata.tsv	Fri Jan 13 22:43:21 2023 +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/emp_single.test0.sequences.qza has changed
Binary file test-data/summarize.test0.demux.qza has changed