pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main
v0.1

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Workflow Type: Galaxy

Pathogens of all samples report generation and visualization

SEEK ID: https://workflowhub.eu/workflows/1060?version=1

DOI: 10.48546/workflowhub.workflow.1060.1

Inputs

ID Name Description Type
amr_identified_by_ncbi amr_identified_by_ncbi output_of_abricate_with_amrfinderncbi
  • File[]
amrs amrs amrs
  • File[]
contigs contigs Contigs
  • File[]
mapping_coverage_percentage_per_sample mapping_coverage_percentage_per_sample mapping_coverage_percentage_per_sample
  • File
mapping_mean_depth_per_sample mapping_mean_depth_per_sample mapping_mean_depth_per_sample
  • File
metadata metadata samples_metadata
  • File?
number_of_variants_per_sample number_of_variants_per_sample number_of_variants_per_sample
  • File
removed_hosts_percentage_tabular removed_hosts_percentage_tabular removed_hosts_percentage_tabular
  • File
vfs vfs VFs
  • File[]
vfs_of_genes_identified_by_vfdb vfs_of_genes_identified_by_vfdb output_of_abricate_with_vfdb
  • File[]

Steps

ID Name Description
10 Filter failed datasets __FILTER_FAILED_DATASETS__
11 Filter failed datasets __FILTER_FAILED_DATASETS__
12 Filter failed datasets __FILTER_FAILED_DATASETS__
13 Filter failed datasets __FILTER_FAILED_DATASETS__
14 Filter failed datasets __FILTER_FAILED_DATASETS__
15 Remove beginning Remove beginning1
16 Remove beginning Remove beginning1
17 Remove beginning Remove beginning1
18 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
19 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
20 Remove beginning Remove beginning1
21 Count Count1
22 Count Count1
23 Group Grouping1
24 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
25 Split by group toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6
26 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
27 Cut Cut1
28 Cut Cut1
29 Filter empty datasets __FILTER_EMPTY_DATASETS__
30 Cut Cut1
31 Cut Cut1
32 Cut Cut1
33 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
34 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
35 Column join toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
36 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
37 Remove beginning Remove beginning1
38 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
39 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
40 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
41 Column Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
42 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
43 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
44 Regex Find And Replace toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
45 Multi-Join toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1
46 Heatmap w ggplot toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0
47 Filter empty datasets __FILTER_EMPTY_DATASETS__
48 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
49 Filter empty datasets __FILTER_EMPTY_DATASETS__
50 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1
51 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
52 Filter empty datasets __FILTER_EMPTY_DATASETS__
53 FASTA-to-Tabular toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
54 Cut Cut1
55 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
56 Cut Cut1
57 Group Grouping1
58 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
59 Group Grouping1
60 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
61 Tabular-to-FASTA toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
62 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
63 FASTA Merge Files and Filter Unique Sequences toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
64 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
65 ClustalW toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
66 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
67 FASTTREE toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
68 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
69 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1

Outputs

ID Name Description Type
all_samples_contigs_in_one_fasta_file all_samples_contigs_in_one_fasta_file n/a
  • File
all_vfs_in_one_tabular all_vfs_in_one_tabular n/a
  • File
split_by_group_collection split_by_group_collection n/a
  • File
adjusted_abricate_vfs_tabular_part1 adjusted_abricate_vfs_tabular_part1 n/a
  • File
adjusted_abricate_vfs_tabular_part2 adjusted_abricate_vfs_tabular_part2 n/a
  • File
amrs_count amrs_count n/a
  • File
vfs_count vfs_count n/a
  • File
heatmap_table heatmap_table n/a
  • File
filtered_sequences_with_vfs_fasta filtered_sequences_with_vfs_fasta n/a
  • File
heatmap_png heatmap_png n/a
  • File
heatmap_pdf heatmap_pdf n/a
  • File
clustalw_on_input_dnd clustalw_on_input_dnd n/a
  • File
clustalw_on_input_clustal clustalw_on_input_clustal n/a
  • File
vfs_amrs_count_table vfs_amrs_count_table n/a
  • File
filtered_empty_datasets filtered_empty_datasets n/a
  • File
fasttree_nhx fasttree_nhx n/a
  • File
newick_genes_tree_graphs_collection newick_genes_tree_graphs_collection n/a
  • File
all_samples_phylogenetic_tree_based_amrs all_samples_phylogenetic_tree_based_amrs n/a
  • File
all_samples_phylogenetic_tree_based_vfs all_samples_phylogenetic_tree_based_vfs n/a
  • File

Version History

v0.1 (earliest) Created 26th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 4657da8
help Creators and Submitter
Creators
  • Engy Nasr
  • Bérénice Batut
  • Paul Zierep
Submitter
Tools
BEDTools
ggplot2
Clustal 2 (Clustal W, Clustal X)
FastTree
Newick Utilities
Citation
Nasr, E., Batut, B., & Zierep, P. (2024). pathogen-detection-pathogfair-samples-aggregation-and-visualisation/main. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.1060.1
License
MIT License (MIT)
Activity

Views: 4532   Downloads: 9177   Runs: 2

Created: 26th Jun 2024 at 03:02

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Total size: 3.65 MB
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