Mercurial > repos > q2d2 > qiime2__composition__tabulate
changeset 0:359aa4321add draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
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date | Fri, 13 Jan 2023 22:04:52 +0000 |
parents | |
children | 54caf7f5c410 |
files | qiime2__composition__tabulate.xml test-data/ancombc.test0.metadata.tsv test-data/ancombc.test0.table.qza test-data/ancombc.test1.metadata.tsv test-data/ancombc.test1.table.qza |
diffstat | 5 files changed, 131 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__composition__tabulate.xml Fri Jan 13 22:04:52 2023 +0000 @@ -0,0 +1,59 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +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: 2022.11.1) +for: + qiime2 (version: 2022.11.1) +--> +<tool name="qiime2 composition tabulate" id="qiime2__composition__tabulate" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> + <description> View tabular output from ANCOM-BC.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.11</container> + </requirements> + <version_command>q2galaxy version composition</version_command> + <command detect_errors="exit_code">q2galaxy run composition tabulate '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="data" type="data" format="qza" label="data: FeatureData[DifferentialAbundance]" help="[required] The ANCOM-BC output to be tabulated."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[DifferentialAbundance]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DifferentialAbundance]']</validator> + </param> + </inputs> + <outputs> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: composition tabulate +============================= + View tabular output from ANCOM-BC. + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Generate tabular view of ANCOM-BC output, which includes per-page views for the log-fold change (lfc), standard error (se), P values, Q values, and W scores. + + +| + +</help> + <citations> + <citation type="doi">10.3402/mehd.v26.27663</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test0.metadata.tsv Fri Jan 13 22:04:52 2023 +0000 @@ -0,0 +1,36 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +L1S8 AGCTGACTAGTC gut 10 28 subject-1 dog test1 value A +L1S57 ACACACTATGGC gut 1 20 subject-1 dog test2 value Z +L1S76 ACTACGTGTGGT gut 2 17 subject-1 cow test1 value Z +L1S105 AGTGCGATGCGT gut 3 17 subject-1 cat test2 value A +L2S155 ACGATGCGACCA left palm 1 20 subject-1 cat test1 value A +L2S175 AGCTATCCACGA left palm 2 17 subject-1 cat test2 value A +L2S204 ATGCAGCTCAGT left palm 3 17 subject-1 bird test1 value Z +L2S222 CACGTGACATGT left palm 4 14 subject-1 cow test2 value Z +L3S242 ACAGTTGCGCGA right palm 10 28 subject-1 bird test1 value A +L3S294 CACGACAGGCTA right palm 1 20 subject-1 dog test2 value Z +L3S313 AGTGTCACGGTG right palm 2 17 subject-1 dog test1 value Z +L3S341 CAAGTGAGAGAG right palm 3 17 subject-1 cat test2 value Z +L3S360 CATCGTATCAAC right palm 4 14 subject-1 cat test1 value A +L5S104 CAGTGTCAGGAC tongue 10 28 subject-1 bird test2 value A +L5S155 ATCTTAGACTGC tongue 1 20 subject-1 cow test1 value Z +L5S174 CAGACATTGCGT tongue 2 17 subject-1 dog test2 value A +L5S203 CGATGCACCAGA tongue 3 17 subject-1 cat test1 value Z +L5S222 CTAGAGACTCTT tongue 4 14 subject-1 bird test2 value Z +L1S140 ATGGCAGCTCTA gut 10 28 subject-2 dog test1 value Z +L1S208 CTGAGATACGCG gut 1 20 subject-2 dog test2 value A +L1S257 CCGACTGAGATG gut 3 17 subject-2 dog test1 value A +L1S281 CCTCTCGTGATC gut 4 14 subject-2 cat test2 value Z +L2S240 CATATCGCAGTT left palm 10 28 subject-2 cat test1 value A +L2S309 CGTGCATTATCA left palm 1 20 subject-2 cat test2 value A +L2S357 CTAACGCAGTCA left palm 3 17 subject-2 bird test1 value Z +L2S382 CTCAATGACTCA left palm 4 14 subject-2 bird test2 value A +L3S378 ATCGATCTGTGG right palm 10 28 subject-2 cow test1 value Z +L4S63 CTCGTGGAGTAG right palm 1 20 subject-2 dog test2 value Z +L4S112 GCGTTACACACA right palm 3 17 subject-2 cat test1 value A +L4S137 GAACTGTATCTC right palm 4 14 subject-2 bird test2 value A +L5S240 CTGGACTCATAG tongue 10 28 subject-2 dog test1 value A +L6S93 GCGTTACACACA tongue 3 17 subject-2 dog test1 value Z +L6S20 GAACTGTATCTC tongue 4 14 subject-2 bird test2 value Z +L6S68 CTGGACTCATAG gut 10 28 subject-2 cow test1 value Z
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ancombc.test1.metadata.tsv Fri Jan 13 22:04:52 2023 +0000 @@ -0,0 +1,36 @@ +sample-id barcode-sequence bodysite month day subject animal testcolumn singlecolumn AZcolumn +#q2:types categorical categorical numeric numeric categorical categorical categorical categorical categorical +L1S8 AGCTGACTAGTC gut 10 28 subject-1 dog test1 value A +L1S57 ACACACTATGGC gut 1 20 subject-1 dog test2 value Z +L1S76 ACTACGTGTGGT gut 2 17 subject-1 cow test1 value Z +L1S105 AGTGCGATGCGT gut 3 17 subject-1 cat test2 value A +L2S155 ACGATGCGACCA left palm 1 20 subject-1 cat test1 value A +L2S175 AGCTATCCACGA left palm 2 17 subject-1 cat test2 value A +L2S204 ATGCAGCTCAGT left palm 3 17 subject-1 bird test1 value Z +L2S222 CACGTGACATGT left palm 4 14 subject-1 cow test2 value Z +L3S242 ACAGTTGCGCGA right palm 10 28 subject-1 bird test1 value A +L3S294 CACGACAGGCTA right palm 1 20 subject-1 dog test2 value Z +L3S313 AGTGTCACGGTG right palm 2 17 subject-1 dog test1 value Z +L3S341 CAAGTGAGAGAG right palm 3 17 subject-1 cat test2 value Z +L3S360 CATCGTATCAAC right palm 4 14 subject-1 cat test1 value A +L5S104 CAGTGTCAGGAC tongue 10 28 subject-1 bird test2 value A +L5S155 ATCTTAGACTGC tongue 1 20 subject-1 cow test1 value Z +L5S174 CAGACATTGCGT tongue 2 17 subject-1 dog test2 value A +L5S203 CGATGCACCAGA tongue 3 17 subject-1 cat test1 value Z +L5S222 CTAGAGACTCTT tongue 4 14 subject-1 bird test2 value Z +L1S140 ATGGCAGCTCTA gut 10 28 subject-2 dog test1 value Z +L1S208 CTGAGATACGCG gut 1 20 subject-2 dog test2 value A +L1S257 CCGACTGAGATG gut 3 17 subject-2 dog test1 value A +L1S281 CCTCTCGTGATC gut 4 14 subject-2 cat test2 value Z +L2S240 CATATCGCAGTT left palm 10 28 subject-2 cat test1 value A +L2S309 CGTGCATTATCA left palm 1 20 subject-2 cat test2 value A +L2S357 CTAACGCAGTCA left palm 3 17 subject-2 bird test1 value Z +L2S382 CTCAATGACTCA left palm 4 14 subject-2 bird test2 value A +L3S378 ATCGATCTGTGG right palm 10 28 subject-2 cow test1 value Z +L4S63 CTCGTGGAGTAG right palm 1 20 subject-2 dog test2 value Z +L4S112 GCGTTACACACA right palm 3 17 subject-2 cat test1 value A +L4S137 GAACTGTATCTC right palm 4 14 subject-2 bird test2 value A +L5S240 CTGGACTCATAG tongue 10 28 subject-2 dog test1 value A +L6S93 GCGTTACACACA tongue 3 17 subject-2 dog test1 value Z +L6S20 GAACTGTATCTC tongue 4 14 subject-2 bird test2 value Z +L6S68 CTGGACTCATAG gut 10 28 subject-2 cow test1 value Z