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 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 |
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License
All versions of this Workflow are
licensed under:
MIT License
Version 5
(of 9)
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