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.
Preview
Not available
Import
Not currently available.
Workflow Components
Inputs (21)
Name |
Description |
Host Genome |
|
FASTQ Forward |
|
input1 |
runtime parameter for tool BAM-to-SAM |
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 |
sam_type |
runtime parameter for tool SNPFinder |
reference |
runtime parameter for tool SNPFinder |
Annotation Database |
|
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 |
Steps (18)
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 |
|
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 |
|
SNPFinder |
toolshed.g2.bx.psu.edu/repos/chrisd/snpfinder/snpfinder/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 |
|
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 (26)
Name |
Type |
output1 |
sam |
gene |
tabular |
mech |
tabular |
class |
tabular |
group |
tabular |
gene |
tabular |
mech |
tabular |
class |
tabular |
group |
tabular |
output |
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 |
output1 |
bam |
Uploader
License
All versions of this Workflow are
licensed under:
MIT License
Version 2 (latest)
(of 2)
Credits (1)
(People/Groups)
Attributions (0)
(Workflows/Files)
None
Shared with Groups (0)
None
Featured In Packs (0)
None
Log in to add to one of your Packs
Attributed By (0)
(Workflows/Files)
None
Favourited By (0)
No one
Statistics
Other workflows that use similar services
(0)
There are no workflows in myExperiment that use similar services to this Workflow.
Comments (0)
No comments yet
Log in to make a comment