Mercurial > repos > nml > mob_suite

annotate workflows/AMRworkflow_STARAMR.ga @ 3:066b2a1c6a55 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
author nml
date Mon, 20 Aug 2018 15:04:54 -0400
parents 2c7f721a4905
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
1 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
2 "a_galaxy_workflow": "true",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
3 "annotation": "Mobilome and resistome analyses are valuable tools to better characterize genome assemblies for the presence of antibiotic resistance phenotypes and mobile elements such as plasmids. The location of the resistance (chromosome or plasmid) will provide information on potential dissemination potential of the antibiotic resistance genes via horizontal or clonal gene transfer mechanisms (available via the summary.tsv report). This draft workflow will help end-user to potentially qualitatively estimate potential AMR risk for a given isolate along with the underlying mechanisms and the epidemiology of antimicrobial resistance. \n\nPlease provide us with your feedback in order to improve usability and flexibility of the workflow. For more information refer to http://dx.doi.org/10.1099/mgen.0.000206 and https://github.com/phac-nml/staramr. \n\n",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
4 "format-version": "0.1",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
5 "name": "Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR)",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
6 "steps": {
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
7 "0": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
8 "annotation": "",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
9 "content_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
10 "errors": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
11 "id": 0,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
12 "input_connections": {},
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
13 "inputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
14 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
15 "description": "runtime parameter for tool MOB-Recon",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
16 "name": "input"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
17 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
18 ],
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
19 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
20 "name": "MOB-Recon",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
21 "outputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
22 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
23 "name": "seqhits",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
24 "type": "input"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
25 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
26 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
27 "name": "outfile1",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
28 "type": "tabular"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
29 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
30 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
31 "name": "outfile2",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
32 "type": "tabular"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
33 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
34 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
35 "name": "outfile3",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
36 "type": "tabular"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
37 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
38 ],
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
39 "position": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
40 "left": 200,
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
41 "top": 200
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
42 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
43 "post_job_actions": {
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
44 "HideDatasetActionoutfile1": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
45 "action_arguments": {},
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
46 "action_type": "HideDatasetAction",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
47 "output_name": "outfile1"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
48 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
49 "HideDatasetActionoutfile2": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
50 "action_arguments": {},
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
51 "action_type": "HideDatasetAction",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
52 "output_name": "outfile2"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
53 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
54 "HideDatasetActionoutfile3": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
55 "action_arguments": {},
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
56 "action_type": "HideDatasetAction",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
57 "output_name": "outfile3"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
58 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
59 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
60 "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.8",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
61 "tool_shed_repository": {
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
62 "changeset_revision": "2c7f721a4905",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
63 "name": "mob_suite",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
64 "owner": "nml",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
65 "tool_shed": "toolshed.g2.bx.psu.edu"
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
66 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
67 "tool_state": "{\"adv_param\": \"{\\\"min_length_condition\\\": {\\\"min_length_param\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"min_con_ident\\\": \\\"80\\\", \\\"min_mob_ident\\\": \\\"80\\\", \\\"min_mob_evalue\\\": \\\"1e-05\\\", \\\"min_rep_evalue\\\": \\\"1e-05\\\", \\\"unicycler_contigs\\\": \\\"True\\\", \\\"min_rep_ident\\\": \\\"80\\\", \\\"min_rpp_evalue\\\": \\\"1e-05\\\", \\\"min_rpp_ident\\\": \\\"80\\\", \\\"run_circlator\\\": \\\"True\\\", \\\"min_con_evalue\\\": \\\"1e-05\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__page__\": null}",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
68 "tool_version": "1.4.8",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
69 "type": "tool",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
70 "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
71 "workflow_outputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
72 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
73 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
74 "output_name": "seqhits",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
75 "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
76 }
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
77 ]
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
78 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
79 "1": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
80 "annotation": "",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
81 "content_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.2.2",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
82 "errors": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
83 "id": 1,
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
84 "input_connections": {
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
85 "genomes": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
86 "id": 0,
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
87 "output_name": "seqhits"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
88 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
89 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
90 "inputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
91 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
92 "description": "runtime parameter for tool staramr",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
93 "name": "genomes"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
94 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
95 ],
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
96 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
97 "name": "staramr",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
98 "outputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
99 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
100 "name": "blast_hits",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
101 "type": "input"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
102 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
103 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
104 "name": "summary",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
105 "type": "tabular"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
106 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
107 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
108 "name": "resfinder",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
109 "type": "tabular"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
110 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
111 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
112 "name": "pointfinder",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
113 "type": "tabular"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
114 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
115 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
116 "name": "settings",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
117 "type": "txt"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
118 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
119 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
120 "name": "excel",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
121 "type": "xlsx"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
122 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
123 ],
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
124 "position": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
125 "left": 420,
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
126 "top": 200
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
127 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
128 "post_job_actions": {
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
129 "HideDatasetActionpointfinder": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
130 "action_arguments": {},
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
131 "action_type": "HideDatasetAction",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
132 "output_name": "pointfinder"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
133 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
134 "HideDatasetActionsettings": {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
135 "action_arguments": {},
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
136 "action_type": "HideDatasetAction",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
137 "output_name": "settings"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
138 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
139 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
140 "tool_id": "toolshed.g2.bx.psu.edu/repos/nml/staramr/staramr_search/0.2.2",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
141 "tool_shed_repository": {
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
142 "changeset_revision": "9047a1d3d8ea",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
143 "name": "staramr",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
144 "owner": "nml",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
145 "tool_shed": "toolshed.g2.bx.psu.edu"
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
146 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
147 "tool_state": "{\"__page__\": null, \"use_pointfinder\": \"{\\\"enable\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"genomes\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"advanced\": \"{\\\"pid_threshold\\\": \\\"98.0\\\", \\\"exclude_resistance_phenotypes\\\": \\\"false\\\", \\\"exclude_negatives\\\": \\\"false\\\", \\\"plength_resfinder\\\": \\\"60.0\\\", \\\"plength_pointfinder\\\": \\\"95.0\\\", \\\"report_all_blast\\\": \\\"false\\\"}\"}",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
148 "tool_version": "0.2.2",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
149 "type": "tool",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
150 "uuid": "41f8718f-87a0-45d2-b79d-e5afddea1532",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
151 "workflow_outputs": [
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
152 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
153 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
154 "output_name": "blast_hits",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
155 "uuid": "9e8592ad-71c0-4528-8e8b-efcd3bb9183a"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
156 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
157 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
158 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
159 "output_name": "resfinder",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
160 "uuid": "2f27a46b-29bf-4abf-9d26-fce4e9fc9dd5"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
161 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
162 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
163 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
164 "output_name": "excel",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
165 "uuid": "67549d0b-0480-4c25-8bfd-1fa78cfdb066"
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
166 },
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
167 {
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
168 "label": null,
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
169 "output_name": "summary",
2
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
170 "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7"
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
171 }
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
172 ]
2c7f721a4905 planemo upload for repository https://github.com/phac-nml/mob-suite commit eecf57ea6130c483487087554c53918fe2b556dd
nml
parents:
diff changeset
173 }
3
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
174 },
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
175 "tags": [
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
176 "AMR",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
177 "Resistance",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
178 "ResFinder",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
179 "StarAMR",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
180 "MOB-Suite",
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
181 "ARGs"
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
182 ],
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
183 "uuid": "d6ce87c0-2d16-4c8c-bea8-6464264565d4"
066b2a1c6a55 planemo upload for repository https://github.com/phac-nml/mob-suite commit 0d017a04a662d1afcd154712ebb699860341af45
nml
parents: 2
diff changeset
184 }