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Changeset 0:287d3ad1a25f (2024-04-25)

Next changeset 1:a0b7ea0bc025 (2024-06-03)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 000000000000 -r 287d3ad1a25f qiime2__feature_table__tabulate_sample_frequencies.xml
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[

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+<?xml version='1.0' encoding='utf-8'?>
+
+
+<tool name="qiime2 feature-table tabulate-sample-frequencies" id="qiime2__feature_table__tabulate_sample_frequencies" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
+    <description>Tabulate sample frequencies</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="exit_code">q2galaxy run feature_table tabulate_sample_frequencies '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]" help="[required]  The input feature table.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="sample_frequencies" format="qza" label="${tool.name} on ${on_string}: sample_frequencies.qza" from_work_dir="sample_frequencies.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="tabulate_sample_frequencies.test0.feature-table.qza" ftype="qza"/>
+            <output name="sample_frequencies" 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: ImmutableMetadata"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+QIIME 2: feature-table tabulate-sample-frequencies
+==================================================
+Tabulate sample frequencies
+
+
+Outputs:
+--------
+:sample_frequencies.qza: Observed feature count and total frequencies per sample.
+
+|
+
+Description:
+------------
+Tabulate feature count and total frequency per sample.
+
+Examples:
+---------
+
+feature_table_tabulate_sample_frequencies
+*****************************************
+Using the ``qiime2 feature-table tabulate-sample-frequencies`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Press the ``Execute`` button.
+
+
+
+|
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>

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+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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+GG1
+GG2

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