Mercurial > repos > nml > mob_suite

comparison workflows/AMRworkflow_STARAMR.ga @ 2:2c7f721a4905 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 eecf57ea6130c483487087554c53918fe2b556dd
author nml
date Fri, 17 Aug 2018 11:12:08 -0400
parents
children 066b2a1c6a55
comparison
equal deleted inserted replaced
1:2c419df5cdaa 2:2c7f721a4905
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "AMRworkflow",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "content_id": "mob_recon",
10 "errors": null,
11 "id": 0,
12 "input_connections": {},
13 "inputs": [
14 {
15 "description": "runtime parameter for tool MOB-Recon",
16 "name": "input"
17 }
18 ],
19 "label": null,
20 "name": "MOB-Recon",
21 "outputs": [
22 {
23 "name": "seqhits",
24 "type": "input"
25 },
26 {
27 "name": "outfile1",
28 "type": "tabular"
29 },
30 {
31 "name": "outfile2",
32 "type": "tabular"
33 },
34 {
35 "name": "outfile3",
36 "type": "tabular"
37 }
38 ],
39 "position": {
40 "left": 200,
41 "top": 200
42 },
43 "post_job_actions": {
44 "HideDatasetActionoutfile1": {
45 "action_arguments": {},
46 "action_type": "HideDatasetAction",
47 "output_name": "outfile1"
48 },
49 "HideDatasetActionoutfile2": {
50 "action_arguments": {},
51 "action_type": "HideDatasetAction",
52 "output_name": "outfile2"
53 },
54 "HideDatasetActionoutfile3": {
55 "action_arguments": {},
56 "action_type": "HideDatasetAction",
57 "output_name": "outfile3"
58 }
59 },
60 "tool_id": "mob_recon",
61 "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}",
62 "tool_version": "1.4.8",
63 "type": "tool",
64 "uuid": "017d5861-8836-46a8-8444-0dcaca60eda1",
65 "workflow_outputs": [
66 {
67 "label": null,
68 "output_name": "seqhits",
69 "uuid": "6304bc2b-bcc9-47c4-8e3b-9d2ee5a80433"
70 }
71 ]
72 },
73 "1": {
74 "annotation": "",
75 "content_id": "staramr_search",
76 "errors": null,
77 "id": 1,
78 "input_connections": {
79 "genomes": {
80 "id": 0,
81 "output_name": "seqhits"
82 }
83 },
84 "inputs": [
85 {
86 "description": "runtime parameter for tool staramr",
87 "name": "genomes"
88 }
89 ],
90 "label": null,
91 "name": "staramr",
92 "outputs": [
93 {
94 "name": "blast_hits",
95 "type": "input"
96 },
97 {
98 "name": "summary",
99 "type": "tabular"
100 },
101 {
102 "name": "resfinder",
103 "type": "tabular"
104 },
105 {
106 "name": "pointfinder",
107 "type": "tabular"
108 },
109 {
110 "name": "settings",
111 "type": "txt"
112 },
113 {
114 "name": "excel",
115 "type": "xlsx"
116 }
117 ],
118 "position": {
119 "left": 420,
120 "top": 200
121 },
122 "post_job_actions": {
123 "HideDatasetActionpointfinder": {
124 "action_arguments": {},
125 "action_type": "HideDatasetAction",
126 "output_name": "pointfinder"
127 },
128 "HideDatasetActionsettings": {
129 "action_arguments": {},
130 "action_type": "HideDatasetAction",
131 "output_name": "settings"
132 }
133 },
134 "tool_id": "staramr_search",
135 "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\\\"}\"}",
136 "tool_version": "0.2.2",
137 "type": "tool",
138 "uuid": "41f8718f-87a0-45d2-b79d-e5afddea1532",
139 "workflow_outputs": [
140 {
141 "label": null,
142 "output_name": "blast_hits",
143 "uuid": "9e8592ad-71c0-4528-8e8b-efcd3bb9183a"
144 },
145 {
146 "label": null,
147 "output_name": "resfinder",
148 "uuid": "2f27a46b-29bf-4abf-9d26-fce4e9fc9dd5"
149 },
150 {
151 "label": null,
152 "output_name": "excel",
153 "uuid": "67549d0b-0480-4c25-8bfd-1fa78cfdb066"
154 },
155 {
156 "label": null,
157 "output_name": "summary",
158 "uuid": "17c9e48c-234a-4cb7-986d-f88166bfe0a7"
159 }
160 ]
161 }
162 },
163 "tags": [],
164 "uuid": "4c695847-5fc7-4020-a125-a500700ab320"
165 }