Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
3.0 (earliest)

2.0 (latest)

3.0 (earliest)

Workflow Type: Galaxy

Pathogens of all samples report generation and visualization

Associated Tutorial

This workflows is part of the tutorial Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation, available in the GTN

Features

Includes a Galaxy Workflow Report
Uses Galaxy Workflow Comments

Thanks to...

Tutorial Author(s): Bérénice Batut, Engy Nasr, Paul Zierep

Tutorial Contributor(s): Hans-Rudolf Hotz, Wolfgang Maier

Workflow Author(s): Engy Nasr, Bérénice Batut, Paul Zierep

Funder(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health, EOSC-Life

SEEK ID: https://dev.workflowhub.eu/workflows/1077?version=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	Bar chart	barchart_gnuplot
13	Bar chart	barchart_gnuplot
14	Bar chart	barchart_gnuplot
15	Filter failed datasets	__FILTER_FAILED_DATASETS__
16	Bar chart	barchart_gnuplot
17	Bar chart	barchart_gnuplot
18	Filter failed datasets	__FILTER_FAILED_DATASETS__
19	Filter failed datasets	__FILTER_FAILED_DATASETS__
20	Remove beginning	Remove beginning1
21	Remove beginning	Remove beginning1
22	Remove beginning	Remove beginning1
23	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
24	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
25	Remove beginning	Remove beginning1
26	Count	Count1
27	Count	Count1
28	Group	Grouping1
29	Unique	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
30	Split by group	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6
31	Unique	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1
32	Cut	Cut1
33	Cut	Cut1
34	Filter empty datasets	__FILTER_EMPTY_DATASETS__
35	Cut	Cut1
36	Cut	Cut1
37	Cut	Cut1
38	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
39	Collapse Collection	toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
40	Column join	toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3
41	bedtools getfasta	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
42	Remove beginning	Remove beginning1
43	bedtools getfasta	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
44	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
45	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
46	Column Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
47	Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
48	bedtools getfasta	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1
49	Regex Find And Replace	toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3
50	Multi-Join	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/9.3+galaxy1
51	Heatmap w ggplot	toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/3.4.0+galaxy0
52	Filter empty datasets	__FILTER_EMPTY_DATASETS__
53	ClustalW	toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
54	Filter empty datasets	__FILTER_EMPTY_DATASETS__
55	Replace Text	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1
56	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
57	Filter empty datasets	__FILTER_EMPTY_DATASETS__
58	FASTA-to-Tabular	toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.1
59	Cut	Cut1
60	FASTTREE	toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
61	Cut	Cut1
62	Group	Grouping1
63	Newick Display	toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
64	Group	Grouping1
65	Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
66	Tabular-to-FASTA	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
67	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
68	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
69	ClustalW	toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
70	ClustalW	toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1+galaxy1
71	FASTTREE	toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
72	FASTTREE	toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10+galaxy1
73	Newick Display	toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1
74	Newick Display	toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6+galaxy1

Outputs

ID	Name	Description	Type
number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig	number_of_reads_before_host_removal_and_number_of_host_reads_found_per_sample_fig	n/a	File
removed_host_percentage_fig	removed_host_percentage_fig	n/a	File
mapping_mean_depth_per_sample_fig	mapping_mean_depth_per_sample_fig	n/a	File
mapping_coverage_percentage_per_sample_fig	mapping_coverage_percentage_per_sample_fig	n/a	File
number_of_Variants_and_SNPs_indentified_fig	number_of_Variants_and_SNPs_indentified_fig	n/a	File
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_pdf	heatmap_pdf	n/a	File
heatmap_png	heatmap_png	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