16S_biodiversity_for_overlap_paired_end
Version 1

Workflow Type: Galaxy
Stable

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

Inputs

ID Name Description Type
"Input Dataset Collection" "Input Dataset Collection" n/a n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a
adapters adapters runtime parameter for tool FastQC n/a
contaminants contaminants runtime parameter for tool FastQC n/a
limits limits runtime parameter for tool FastQC n/a
dbfile dbfile runtime parameter for tool VSearch search n/a
output output runtime parameter for tool Convert n/a
output output runtime parameter for tool Convert 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 Phyloseq 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 "Input Dataset Collection"
1 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
2 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6
3 Pear toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5 Concatenate datasets cat1
6 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
7 MergeSamFiles toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1
8 FilterSamReads toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1
9 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
10 VSearch search toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
11 VSearch dereplication toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/2.8.3.0
12 VSearch chimera detection toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/2.8.3.0
13 VSearch clustering toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0
14 VSearch search toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
15 Add column addValue
16 Cut Cut1
17 Cut Cut1
18 Concatenate datasets cat1
19 OTUTable toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_uc2otutable/uclust2otutable/1.0.0
20 Convert toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.5.3
21 BIOM metadata toolshed.g2.bx.psu.edu/repos/iuc/biom_add_metadata/biom_add_metadata/2.1.5.0
22 Phyloseq DESeq2 toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_deseq2/phyloseq_DESeq2/1.22.3
23 Phyloseq Richness toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_richness/phyloseq_richness/1.22.3.2
24 Phyloseq Abundance plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_factor/phyloseq_abundance/1.22.3.3
25 Phyloseq Abundance Taxonomy toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_taxonomy/phyloseq_taxonomy/1.22.3.3
26 Symmetric Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_symmetric_plot/symmetricPlot/1.0.1
27 Phyloseq Network Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_net/phyloseq_net/1.24.2

Outputs

ID Name Description Type
html_file html_file n/a
text_file text_file n/a
fastq_out_paired fastq_out_paired n/a
fastq_out_unpaired fastq_out_unpaired n/a
assembled_reads assembled_reads n/a
html_file html_file n/a
text_file text_file n/a
out_file1 out_file1 n/a
bam_output bam_output n/a
outFile outFile n/a
outFile outFile n/a
output output n/a
uc uc n/a
notmatched notmatched n/a
matched matched n/a
outfile outfile n/a
outfile outfile n/a
nonchimeras nonchimeras n/a
consout consout n/a
uc uc n/a
notmatched notmatched n/a
matched matched n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
out_file1 out_file1 n/a
output output n/a
output_fp output_fp n/a
output_table output_table n/a
DE_table DE_table n/a
normalised_table normalised_table n/a
htmlfile htmlfile n/a
htmlfile htmlfile n/a
htmlfile htmlfile n/a
htmlfile htmlfile n/a
htmlfile htmlfile n/a
Total size: 61.5 KB
help Creators and Submitter
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Views: 185   Downloads: 3

Created: 10th Nov 2021 at 00:15

Last used: 25th Jan 2022 at 04:29

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Version History

Version 1 (earliest) Created 10th Nov 2021 at 00:15 by Mike Thang

Added/updated 1 files


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