AmrPlusPlus Single Workflow
Created: 2016-08-12 00:45:39
Last updated: 2017-01-05 18:57:14
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 (16)
Name |
Description |
FASTQ Forward |
|
Host Genome |
|
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 |
AMR Database |
|
paired_end |
runtime parameter for tool Trimmomatic |
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 |
input1 |
runtime parameter for tool BAM-to-SAM |
Steps (12)
Name |
Tool |
Description |
Input dataset |
None |
|
Input dataset |
None |
|
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 |
|
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 |
|
BAM-to-SAM |
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0 |
|
Outputs (15)
Name |
Type |
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 |
output1 |
sam |
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License
All versions of this Workflow are
licensed under:
MIT License
Version 1 (earliest)
(of 2)
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