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 and virulence factors from metagenomic sequence data.

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Workflow Components

Inputs (17)

Name	Description
FASTQ Forward
FASTQ Reverse
input1	runtime parameter for tool BAM-to-SAM
sam_type	runtime parameter for tool Snip Finder
reference	runtime parameter for tool Snip Finder
reference	runtime parameter for tool Coverage Sampler
sam	runtime parameter for tool Coverage Sampler
Host Genome
AMR 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
input1	runtime parameter for tool Sort

Steps (13)

Name	Tool	Description
Input dataset	None
Input dataset	None
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
Coverage Sampler	toolshed.g2.bx.psu.edu/repos/chrisd/coverage_sampler/gene_fraction/0.1.0
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
Sort	toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0

Outputs (15)

Name	Type
output1	sam
output	tabular
output	tabular
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
output1	bam

Information Workflow Type

Galaxy

Information Uploader

Chris

Information License

All versions of this Workflow are licensed under:

MIT License

Information Version 3 (of 9)

Information Credits (1)

(People/Groups)

Chris

Information Attributions (0)

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None

Information Tags (3)

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Information Statistics

5701 viewings

1203 downloads

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Citations (0)

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Version History

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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