AmrPlusPlus Paired Workflow
Created: 2016-08-05 06:08:44
Last updated: 2016-11-18 05:56:11
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 MetaSNP |
| reference |
runtime parameter for tool MetaSNP |
| 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 |
|
| MetaSNP |
toolshed.g2.bx.psu.edu/repos/chrisd/metasnp/metasnp/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 |
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License
All versions of this Workflow are
licensed under:
MIT License
Version 1 (earliest)
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