AmrPlusPlus Paired Workflow

Created: 2016-08-05 06:08:44 Last updated: 2016-11-18 05:56:11

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AmrPlusPlus is a Galaxy-based metagenomics pipeline that is intuitive and easy to use. The pipeline takes advantage of current and new tools to help identify and characterize resistance genes from metagenomic sequence data.

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Workflow Components

Inputs (22)

Name	Description
Host Genome
FASTQ Forward
input1	runtime parameter for tool Sort
input1	runtime parameter for tool BAM-to-SAM
sam_type	runtime parameter for tool Snip Finder
reference	runtime parameter for tool Snip Finder
sam	runtime parameter for tool ResistomeAnalyzer
annotation	runtime parameter for tool ResistomeAnalyzer
reference	runtime parameter for tool ResistomeAnalyzer
reference	runtime parameter for tool RarefactionAnalyzer
sam	runtime parameter for tool RarefactionAnalyzer
annotation	runtime parameter for tool RarefactionAnalyzer
FASTQ Reverse
AMR Database
Annotation Database
input_type	runtime parameter for tool Map with BWA
input_type	runtime parameter for tool Map with BWA
reference_source	runtime parameter for tool Map with BWA
input	runtime parameter for tool Samtools flag_filter
input1	runtime parameter for tool Sort
input_type	runtime parameter for tool Map with BWA
reference_source	runtime parameter for tool Map with BWA

Steps (19)

Name	Tool	Description
Input dataset	None
Input dataset	None
Sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0
BAM-to-SAM	toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0
Snip Finder	toolshed.g2.bx.psu.edu/repos/chrisd/snipfinder/snipfinder/0.1.0
ResistomeAnalyzer	toolshed.g2.bx.psu.edu/repos/chrisd/resistome_analyzer/resistome_analyzer/0.1.0
RarefactionAnalyzer	toolshed.g2.bx.psu.edu/repos/chrisd/rarefaction_analyzer/rarefaction_analyzer/0.1.0
Plotting tool	toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1
Plotting tool	toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1
Plotting tool	toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1
Plotting tool	toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1
Input dataset	None
Input dataset	None
Input dataset	None
Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3
Map with BWA	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1
Samtools flag_filter	toolshed.g2.bx.psu.edu/repos/brenninc/samtools_flag_filter_1_2/samtools_flag_filter/0.1
Sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0
Map with BWA	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.12.1

Outputs (26)

Name	Type
output1	bam
output1	sam
output	tabular
gene	tabular
mech	tabular
class	tabular
group	tabular
gene	tabular
mech	tabular
class	tabular
group	tabular
out_file1	pdf
out_file1	pdf
out_file1	pdf
out_file1	pdf
fastq_out_paired	input
fastq_out_unpaired	input
fastq_out_r1_paired	fastqsanger
fastq_out_r2_paired	fastqsanger
fastq_out_r1_unpaired	fastqsanger
fastq_out_r2_unpaired	fastqsanger
fastq_out	fastqsanger
bam_output	bam
output	bam
output1	bam
bam_output	bam

Information Workflow Type

Galaxy

Information Uploader

Chris

Information License

All versions of this Workflow are licensed under:

MIT License

Information Version 6 (of 9)

Information Credits (1)

(People/Groups)

Chris

Information Attributions (0)

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None

Information Tags (3)

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Information Attributed By (0)

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Information Favourited By (0)

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Information Statistics

5916 viewings

1272 downloads

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Citations (0)Version History

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In chronological order:

amrplusplus_paired

Created by Chris on Friday 05 August 2016 06:08:43 (UTC)

Last edited by Chris on Friday 05 August 2016 06:12:11 (UTC)
amrplusplus paired workflow

Created by Chris on Friday 05 August 2016 19:19:02 (UTC)

Last edited by Chris on Monday 08 August 2016 00:50:13 (UTC)
amrplusplus paired workflow

Created by Chris on Monday 08 August 2016 00:59:09 (UTC)

Last edited by Chris on Monday 08 August 2016 00:59:29 (UTC)

Revision comment:

Updated input order
amrplusplus paired-end workflow

Created by Chris on Monday 08 August 2016 01:18:58 (UTC)

Last edited by Chris on Sunday 14 August 2016 18:56:15 (UTC)
AmrPlusPlus Paired Workflow

Created by Chris on Sunday 09 October 2016 12:56:50 (UTC)

Revision comment:

Added new tools
AmrPlusPlus Paired Workflow

Created by Chris on Tuesday 11 October 2016 18:13:09 (UTC)

Revision comment:

Updated Resistome Analyzer revision
AmrPlusPlus Paired Workflow

Created by Chris on Tuesday 11 October 2016 18:15:30 (UTC)

Last edited by Chris on Tuesday 11 October 2016 18:16:46 (UTC)
amrplusplus paired-end workflow

Created by Chris on Tuesday 11 October 2016 18:19:23 (UTC)

Last edited by Chris on Saturday 15 October 2016 06:08:12 (UTC)

Revision comment:

Remove import text from workflow title
AmrPlusPlus Paired Workflow

Created by Chris on Friday 18 November 2016 05:56:11 (UTC)

Revision comment:

Update SNPFinder tool to latest revision

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