16S_biodiversity_BIOM
Version 1

Workflow Type: Galaxy
Stable

This is a Galaxy workflow that uses to convert the16S BIOM file to table and figures. It is part of the metaDEGalaxy workflow MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.

Inputs

ID Name Description Type
input_type input_type runtime parameter for tool Convert BIOM n/a
output_type output_type runtime parameter for tool Convert BIOM n/a
output_type output_type runtime parameter for tool Convert BIOM n/a
input_observation_metadata input_observation_metadata runtime parameter for tool BIOM metadata n/a
input_sample_metadata input_sample_metadata runtime parameter for tool BIOM metadata n/a
metadata_input metadata_input runtime parameter for tool DESeq2 n/a
metadata_input metadata_input runtime parameter for tool Phyloseq Richness n/a
metadata_input metadata_input runtime parameter for tool Phyloseq Abundance plot n/a
metadata_input metadata_input runtime parameter for tool Phyloseq Abundance Taxonomy n/a
meta_table meta_table runtime parameter for tool Symmetric Plot n/a
obs_table obs_table runtime parameter for tool Symmetric Plot n/a
file_source file_source runtime parameter for tool Phyloseq Network Plot n/a
metadata_input metadata_input runtime parameter for tool Phyloseq Network Plot n/a

Steps

ID Name Description
0 Convert BIOM toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.5.0
1 BIOM metadata toolshed.g2.bx.psu.edu/repos/iuc/biom_add_metadata/biom_add_metadata/2.1.5.0
2 DESeq2 toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_deseq2/phyloseq_DESeq2/1.22.3
3 Phyloseq Richness toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_richness/phyloseq_richness/1.22.3.2
4 Phyloseq Abundance plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_factor/phyloseq_abundance/1.22.3.3
5 Phyloseq Abundance Taxonomy toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_taxonomy/phyloseq_taxonomy/1.22.3.3
6 Symmetric Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_symmetric_plot/symmetricPlot/1.0.1
7 Phyloseq Network Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_net/phyloseq_net/1.24.2

Outputs

ID Name Description Type
output_table output_table n/a biom1
output_table output_table n/a biom1
DE_table DE_table n/a tabular
normalised_table normalised_table n/a tabular
htmlfile htmlfile n/a html
htmlfile htmlfile n/a html
htmlfile htmlfile n/a html
htmlfile htmlfile n/a html
htmlfile htmlfile n/a html
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Views: 347   Downloads: 3

Created: 11th Aug 2021 at 05:12

Last updated: 11th Aug 2021 at 05:12

Last used: 17th Oct 2021 at 01:27

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Version 1 Created 11th Aug 2021 at 05:12 by Mike Thang

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