| Previous changeset 0:d941f15652f0 (2022-08-29) Next changeset 2:b7b5dc5a067b (2023-06-08) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 69da7976573cc07a363ac66bdacc9269d7cd3732 |
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modified:
qiime2__diversity__alpha_group_significance.xml |
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added:
test-data/alpha_correlation.test0.alpha-div-faith-pd.qza test-data/alpha_correlation.test0.metadata.tsv test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza test-data/alpha_group_significance.test0.metadata.tsv |
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removed:
test-data/.gitkeep |
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| diff -r d941f15652f0 -r 25b94f589fc8 qiime2__diversity__alpha_group_significance.xml --- a/qiime2__diversity__alpha_group_significance.xml Mon Aug 29 19:38:39 2022 +0000 +++ b/qiime2__diversity__alpha_group_significance.xml Fri Jan 13 22:44:33 2023 +0000 |
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| @@ -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 diversity alpha-group-significance" id="qiime2__diversity__alpha_group_significance" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity alpha-group-significance" id="qiime2__diversity__alpha_group_significance" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> <description>Alpha diversity comparisons</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 diversity</version_command> - <command detect_errors="aggressive">q2galaxy run diversity alpha_group_significance '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run diversity alpha_group_significance '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> @@ -45,7 +45,24 @@ <outputs> <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> </outputs> - <tests/> + <tests> + <test> + <param name="alpha_diversity" value="alpha_group_significance.test0.alpha-div-faith-pd.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="alpha_group_significance.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <output name="visualization" ftype="qzv"> + <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: Visualization"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: diversity alpha-group-significance =========================================== @@ -62,6 +79,24 @@ ------------ Visually and statistically compare groups of alpha diversity values. +Examples: +--------- + +alpha_group_significance_faith_pd +********************************* +Using the ``qiime2 diversity alpha-group-significance`` tool: + #. Set *"alpha_diversity"* to ``#: alpha-div-faith-pd.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Press the ``Execute`` button. + + | |
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| diff -r d941f15652f0 -r 25b94f589fc8 test-data/alpha_correlation.test0.alpha-div-faith-pd.qza |
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| Binary file test-data/alpha_correlation.test0.alpha-div-faith-pd.qza has changed |
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| diff -r d941f15652f0 -r 25b94f589fc8 test-data/alpha_correlation.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alpha_correlation.test0.metadata.tsv Fri Jan 13 22:44:33 2023 +0000 |
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| @@ -0,0 +1,50 @@ +sample_name barcode mouse_id genotype cage_id donor donor_status days_post_transplant genotype_and_donor_status +#q2:types categorical categorical categorical categorical categorical categorical numeric categorical +recip.220.WT.OB1.D7 CCTCCGTCATGG 457 wild type C35 hc_1 Healthy 49 wild type and Healthy +recip.290.ASO.OB2.D1 AACAGTAAACAA 456 susceptible C35 hc_1 Healthy 49 susceptible and Healthy +recip.389.WT.HC2.D21 ATGTATCAATTA 435 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D14 GTCAGTATGGCT 435 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.391.ASO.PD2.D21 AGACAGTAGGAG 437 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D7 GGTCTTAGCACC 435 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.400.ASO.HC2.D14 CGTTCGCTAGCC 437 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.401.ASO.HC2.D7 ATTTACAATTGA 437 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.403.ASO.PD2.D21 CGCAGATTAGTA 456 susceptible C35 hc_1 Healthy 21 susceptible and Healthy +recip.411.ASO.HC2.D14 ATGTTAGGGAAT 456 susceptible C35 hc_1 Healthy 14 susceptible and Healthy +recip.411.ASO.HC2.D21 CTCATATGCTAT 457 wild type C35 hc_1 Healthy 21 wild type and Healthy +recip.411.ASO.HC2.D49 GCAACGAACGAG 435 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.412.ASO.HC2.D14 AAGTGGCTATCC 457 wild type C35 hc_1 Healthy 14 wild type and Healthy +recip.412.ASO.HC2.D7 GCATTCGGCGTT 456 susceptible C35 hc_1 Healthy 7 susceptible and Healthy +recip.413.WT.HC2.D7 ACCAGTGACTCA 457 wild type C35 hc_1 Healthy 7 wild type and Healthy +recip.456.ASO.HC3.D49 ACGGCGTTATGT 468 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.458.ASO.HC3.D21 ACGGCCCTGGAG 468 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.458.ASO.HC3.D49 CATTTGACGACG 469 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.459.WT.HC3.D14 ACATGGGCGGAA 468 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.459.WT.HC3.D21 CATAAATTCTTG 469 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.459.WT.HC3.D49 GCTGCGTATACC 536 susceptible C43 pd_1 PD 49 susceptible and PD +recip.460.WT.HC3.D14 CTGCGGATATAC 469 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.460.WT.HC3.D21 GTCAATTAGTGG 536 susceptible C43 pd_1 PD 21 susceptible and PD +recip.460.WT.HC3.D49 GAGAAGCTTATA 537 wild type C43 pd_1 PD 49 wild type and PD +recip.460.WT.HC3.D7 GACCCGTTTCGC 468 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.461.ASO.HC3.D21 AGCCCGCAAAGG 537 wild type C43 pd_1 PD 21 wild type and PD +recip.461.ASO.HC3.D49 GGCGTAACGGCA 538 wild type C44 pd_1 PD 49 wild type and PD +recip.461.ASO.HC3.D7 ATTGCCTTGATT 469 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.462.WT.PD3.D14 GTGAGGGCAAGT 536 susceptible C43 pd_1 PD 14 susceptible and PD +recip.462.WT.PD3.D21 GGCCTATAAGTC 538 wild type C44 pd_1 PD 21 wild type and PD +recip.462.WT.PD3.D49 AATACAGACCTG 539 susceptible C44 pd_1 PD 49 susceptible and PD +recip.462.WT.PD3.D7 TTAGGATTCTAT 536 susceptible C43 pd_1 PD 7 susceptible and PD +recip.463.WT.PD3.D14 ATATTGGCAGCC 537 wild type C43 pd_1 PD 14 wild type and PD +recip.463.WT.PD3.D21 CGCGGCGCAGCT 539 susceptible C44 pd_1 PD 21 susceptible and PD +recip.463.WT.PD3.D7 GTTTATCTTAAG 537 wild type C43 pd_1 PD 7 wild type and PD +recip.464.WT.PD3.D14 TCATCCGTCGGC 538 wild type C44 pd_1 PD 14 wild type and PD +recip.465.ASO.PD3.D14 GGCTTCGGAGCG 539 susceptible C44 pd_1 PD 14 susceptible and PD +recip.465.ASO.PD3.D7 CAGTCTAGTACG 538 wild type C44 pd_1 PD 7 wild type and PD +recip.466.ASO.PD3.D7 GTGGGACTGCGC 539 susceptible C44 pd_1 PD 7 susceptible and PD +recip.467.WT.HC3.D49.a GTCAGGTGCGGC 437 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.467.WT.HC3.D49.b GTTAACTTACTA 546 susceptible C49 pd_1 PD 49 susceptible and PD +recip.536.ASO.PD4.D49 CAAATTCGGGAT 547 wild type C49 pd_1 PD 49 wild type and PD +recip.537.WT.PD4.D21 CTCTATTCCACC 546 susceptible C49 pd_1 PD 21 susceptible and PD +recip.538.WT.PD4.D21 ATGGATAGCTAA 547 wild type C49 pd_1 PD 21 wild type and PD +recip.539.ASO.PD4.D14 GATCCGGCAGGA 546 susceptible C49 pd_1 PD 14 susceptible and PD +recip.539.ASO.PD4.D7 GTTCGAGTGAAT 546 susceptible C49 pd_1 PD 7 susceptible and PD +recip.540.ASO.HC4.D14 CTTCCAACTCAT 547 wild type C49 pd_1 PD 14 wild type and PD +recip.540.ASO.HC4.D7 CGGCCTAAGTTC 547 wild type C49 pd_1 PD 7 wild type and PD |
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| diff -r d941f15652f0 -r 25b94f589fc8 test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza |
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| Binary file test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza has changed |
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| diff -r d941f15652f0 -r 25b94f589fc8 test-data/alpha_group_significance.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alpha_group_significance.test0.metadata.tsv Fri Jan 13 22:44:33 2023 +0000 |
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| @@ -0,0 +1,50 @@ +sample_name barcode mouse_id genotype cage_id donor donor_status days_post_transplant genotype_and_donor_status +#q2:types categorical categorical categorical categorical categorical categorical numeric categorical +recip.220.WT.OB1.D7 CCTCCGTCATGG 457 wild type C35 hc_1 Healthy 49 wild type and Healthy +recip.290.ASO.OB2.D1 AACAGTAAACAA 456 susceptible C35 hc_1 Healthy 49 susceptible and Healthy +recip.389.WT.HC2.D21 ATGTATCAATTA 435 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D14 GTCAGTATGGCT 435 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.391.ASO.PD2.D21 AGACAGTAGGAG 437 susceptible C31 hc_1 Healthy 21 susceptible and Healthy +recip.391.ASO.PD2.D7 GGTCTTAGCACC 435 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.400.ASO.HC2.D14 CGTTCGCTAGCC 437 susceptible C31 hc_1 Healthy 14 susceptible and Healthy +recip.401.ASO.HC2.D7 ATTTACAATTGA 437 susceptible C31 hc_1 Healthy 7 susceptible and Healthy +recip.403.ASO.PD2.D21 CGCAGATTAGTA 456 susceptible C35 hc_1 Healthy 21 susceptible and Healthy +recip.411.ASO.HC2.D14 ATGTTAGGGAAT 456 susceptible C35 hc_1 Healthy 14 susceptible and Healthy +recip.411.ASO.HC2.D21 CTCATATGCTAT 457 wild type C35 hc_1 Healthy 21 wild type and Healthy +recip.411.ASO.HC2.D49 GCAACGAACGAG 435 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.412.ASO.HC2.D14 AAGTGGCTATCC 457 wild type C35 hc_1 Healthy 14 wild type and Healthy +recip.412.ASO.HC2.D7 GCATTCGGCGTT 456 susceptible C35 hc_1 Healthy 7 susceptible and Healthy +recip.413.WT.HC2.D7 ACCAGTGACTCA 457 wild type C35 hc_1 Healthy 7 wild type and Healthy +recip.456.ASO.HC3.D49 ACGGCGTTATGT 468 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.458.ASO.HC3.D21 ACGGCCCTGGAG 468 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.458.ASO.HC3.D49 CATTTGACGACG 469 wild type C42 hc_1 Healthy 49 wild type and Healthy +recip.459.WT.HC3.D14 ACATGGGCGGAA 468 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.459.WT.HC3.D21 CATAAATTCTTG 469 wild type C42 hc_1 Healthy 21 wild type and Healthy +recip.459.WT.HC3.D49 GCTGCGTATACC 536 susceptible C43 pd_1 PD 49 susceptible and PD +recip.460.WT.HC3.D14 CTGCGGATATAC 469 wild type C42 hc_1 Healthy 14 wild type and Healthy +recip.460.WT.HC3.D21 GTCAATTAGTGG 536 susceptible C43 pd_1 PD 21 susceptible and PD +recip.460.WT.HC3.D49 GAGAAGCTTATA 537 wild type C43 pd_1 PD 49 wild type and PD +recip.460.WT.HC3.D7 GACCCGTTTCGC 468 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.461.ASO.HC3.D21 AGCCCGCAAAGG 537 wild type C43 pd_1 PD 21 wild type and PD +recip.461.ASO.HC3.D49 GGCGTAACGGCA 538 wild type C44 pd_1 PD 49 wild type and PD +recip.461.ASO.HC3.D7 ATTGCCTTGATT 469 wild type C42 hc_1 Healthy 7 wild type and Healthy +recip.462.WT.PD3.D14 GTGAGGGCAAGT 536 susceptible C43 pd_1 PD 14 susceptible and PD +recip.462.WT.PD3.D21 GGCCTATAAGTC 538 wild type C44 pd_1 PD 21 wild type and PD +recip.462.WT.PD3.D49 AATACAGACCTG 539 susceptible C44 pd_1 PD 49 susceptible and PD +recip.462.WT.PD3.D7 TTAGGATTCTAT 536 susceptible C43 pd_1 PD 7 susceptible and PD +recip.463.WT.PD3.D14 ATATTGGCAGCC 537 wild type C43 pd_1 PD 14 wild type and PD +recip.463.WT.PD3.D21 CGCGGCGCAGCT 539 susceptible C44 pd_1 PD 21 susceptible and PD +recip.463.WT.PD3.D7 GTTTATCTTAAG 537 wild type C43 pd_1 PD 7 wild type and PD +recip.464.WT.PD3.D14 TCATCCGTCGGC 538 wild type C44 pd_1 PD 14 wild type and PD +recip.465.ASO.PD3.D14 GGCTTCGGAGCG 539 susceptible C44 pd_1 PD 14 susceptible and PD +recip.465.ASO.PD3.D7 CAGTCTAGTACG 538 wild type C44 pd_1 PD 7 wild type and PD +recip.466.ASO.PD3.D7 GTGGGACTGCGC 539 susceptible C44 pd_1 PD 7 susceptible and PD +recip.467.WT.HC3.D49.a GTCAGGTGCGGC 437 susceptible C31 hc_1 Healthy 49 susceptible and Healthy +recip.467.WT.HC3.D49.b GTTAACTTACTA 546 susceptible C49 pd_1 PD 49 susceptible and PD +recip.536.ASO.PD4.D49 CAAATTCGGGAT 547 wild type C49 pd_1 PD 49 wild type and PD +recip.537.WT.PD4.D21 CTCTATTCCACC 546 susceptible C49 pd_1 PD 21 susceptible and PD +recip.538.WT.PD4.D21 ATGGATAGCTAA 547 wild type C49 pd_1 PD 21 wild type and PD +recip.539.ASO.PD4.D14 GATCCGGCAGGA 546 susceptible C49 pd_1 PD 14 susceptible and PD +recip.539.ASO.PD4.D7 GTTCGAGTGAAT 546 susceptible C49 pd_1 PD 7 susceptible and PD +recip.540.ASO.HC4.D14 CTTCCAACTCAT 547 wild type C49 pd_1 PD 14 wild type and PD +recip.540.ASO.HC4.D7 CGGCCTAAGTTC 547 wild type C49 pd_1 PD 7 wild type and PD |