/
16S_taxonomic_analysis.cwl
76 lines (65 loc) · 1.89 KB
/
16S_taxonomic_analysis.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
cwlVersion: v1.0
class: Workflow
label: Functional analyis of sequences that match the 16S SSU
requirements:
- class: SchemaDefRequirement
types:
- $import: ../tools/biom-convert-table.yaml
inputs:
16S_matches:
type: File
outputs:
otu_table_summary:
type: File
outputSource: create_otu_text_summary/otu_table_summary
tree:
type: File
outputSource: prune_tree/pruned_tree
biom_json:
type: File
outputSource: convert_new_biom_to_old_biom/result
steps:
pick_closed_reference_otus:
run: ../tools/qiime-pick_closed_reference_otus.cwl
in:
sequences: 16S_matches
out: [ otu_table, otus_tree ]
convert_new_biom_to_old_biom:
run: ../tools/biom-convert.cwl
in:
biom: pick_closed_reference_otus/otu_table
table_type: { default: OTU table }
json: { default: true }
out: [ result ]
convert_new_biom_to_classic:
run: ../tools/biom-convert.cwl
in:
biom: pick_closed_reference_otus/otu_table
header_key: { default: taxonomy }
table_type: { default: OTU table }
tsv: { default: true }
out: [ result ]
create_otu_text_summary:
run: ../tools/biom-summarize_table.cwl
in:
biom: pick_closed_reference_otus/otu_table
out: [ otu_table_summary ]
extract_observations:
run: ../tools/extract_observations.cwl
in:
tsv_otu_table: convert_new_biom_to_classic/result
out: [ observations ]
prune_tree:
run: ../tools/qiime-filter_tree.cwl
in:
tree: pick_closed_reference_otus/otus_tree
tips_or_seqids_to_retain: extract_observations/observations
out: [ pruned_tree ]
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/docs/schema_org_rdfa.html
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"