0
|
1 {
|
|
2 "a_galaxy_workflow": "true",
|
|
3 "annotation": "",
|
|
4 "format-version": "0.1",
|
|
5 "name": "denovo assembly",
|
|
6 "steps": {
|
|
7 "0": {
|
|
8 "annotation": "The input sequence reads.",
|
|
9 "id": 0,
|
|
10 "input_connections": {},
|
|
11 "inputs": [
|
|
12 {
|
|
13 "description": "The input sequence reads.",
|
|
14 "name": "sequence_reads"
|
|
15 }
|
|
16 ],
|
|
17 "label": null,
|
|
18 "name": "Input dataset",
|
|
19 "outputs": [],
|
|
20 "position": {
|
|
21 "left": 200,
|
|
22 "top": 200
|
|
23 },
|
|
24 "tool_errors": null,
|
|
25 "tool_id": null,
|
|
26 "tool_state": "{\"name\": \"sequence_reads\"}",
|
|
27 "tool_version": null,
|
|
28 "type": "data_input",
|
|
29 "user_outputs": [],
|
|
30 "uuid": "7abd13c4-679c-4601-9bdd-4410cdacb932"
|
|
31 },
|
|
32 "1": {
|
|
33 "annotation": "",
|
|
34 "id": 1,
|
|
35 "input_connections": {
|
|
36 "libraries_0|files_0|file_type|unpaired_reads": {
|
|
37 "id": 0,
|
|
38 "output_name": "output"
|
|
39 }
|
|
40 },
|
|
41 "inputs": [],
|
|
42 "label": null,
|
|
43 "name": "spades",
|
|
44 "outputs": [
|
|
45 {
|
|
46 "name": "out_contigs",
|
|
47 "type": "fasta"
|
|
48 },
|
|
49 {
|
|
50 "name": "out_contig_stats",
|
|
51 "type": "tabular"
|
|
52 },
|
|
53 {
|
|
54 "name": "out_scaffolds",
|
|
55 "type": "fasta"
|
|
56 },
|
|
57 {
|
|
58 "name": "out_scaffold_stats",
|
|
59 "type": "tabular"
|
|
60 },
|
|
61 {
|
|
62 "name": "out_log",
|
|
63 "type": "txt"
|
|
64 }
|
|
65 ],
|
|
66 "position": {
|
|
67 "left": 428,
|
|
68 "top": 200
|
|
69 },
|
|
70 "post_job_actions": {},
|
|
71 "tool_errors": null,
|
|
72 "tool_id": "toolshed.g2.bx.psu.edu/repos/lionelguy/spades/spades/1.0",
|
|
73 "tool_state": "{\"__page__\": 0, \"iontorrent\": \"\\\"False\\\"\", \"kmers\": \"\\\"21,33,55,77,99,127\\\"\", \"cov\": \"{\\\"state\\\": \\\"off\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"nanopore\": \"[]\", \"libraries\": \"[{\\\"lib_type\\\": \\\"paired_end\\\", \\\"__index__\\\": 0, \\\"orientation\\\": \\\"fr\\\", \\\"files\\\": [{\\\"file_type\\\": {\\\"type\\\": \\\"unpaired\\\", \\\"unpaired_reads\\\": null, \\\"__current_case__\\\": 2}, \\\"__index__\\\": 0}]}]\", \"onlyassembler\": \"\\\"False\\\"\", \"trustedcontigs\": \"[]\", \"pacbio\": \"[]\", \"sc\": \"\\\"False\\\"\", \"untrustedcontigs\": \"[]\", \"sanger\": \"[]\", \"careful\": \"\\\"True\\\"\"}",
|
|
74 "tool_version": "1.0",
|
|
75 "type": "tool",
|
|
76 "user_outputs": [],
|
|
77 "uuid": "44e3830f-f4ec-4ab0-8fbb-f8076c35e04b"
|
|
78 },
|
|
79 "2": {
|
|
80 "annotation": "",
|
|
81 "id": 2,
|
|
82 "input_connections": {
|
|
83 "input": {
|
|
84 "id": 1,
|
|
85 "output_name": "out_contig_stats"
|
|
86 }
|
|
87 },
|
|
88 "inputs": [],
|
|
89 "label": null,
|
|
90 "name": "Column Regex Find And Replace",
|
|
91 "outputs": [
|
|
92 {
|
|
93 "name": "out_file1",
|
|
94 "type": "input"
|
|
95 }
|
|
96 ],
|
|
97 "position": {
|
|
98 "left": 731,
|
|
99 "top": 200
|
|
100 },
|
|
101 "post_job_actions": {},
|
|
102 "tool_errors": null,
|
|
103 "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regexColumn1/0.1.0",
|
|
104 "tool_state": "{\"__page__\": 0, \"field\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\"0.000000000000000001\\\", \\\"pattern\\\": \\\"^0$\\\"}]\", \"input\": \"null\"}",
|
|
105 "tool_version": "0.1.0",
|
|
106 "type": "tool",
|
|
107 "user_outputs": [],
|
|
108 "uuid": "59b56d9b-094b-41e8-9572-6e4708379e66"
|
|
109 },
|
|
110 "3": {
|
|
111 "annotation": "",
|
|
112 "id": 3,
|
|
113 "input_connections": {
|
|
114 "fasta_input": {
|
|
115 "id": 1,
|
|
116 "output_name": "out_contigs"
|
|
117 },
|
|
118 "tab_input": {
|
|
119 "id": 2,
|
|
120 "output_name": "out_file1"
|
|
121 }
|
|
122 },
|
|
123 "inputs": [],
|
|
124 "label": null,
|
|
125 "name": "Filter SPAdes repeats",
|
|
126 "outputs": [
|
|
127 {
|
|
128 "name": "output_with_repeats",
|
|
129 "type": "fasta"
|
|
130 },
|
|
131 {
|
|
132 "name": "output_without_repeats",
|
|
133 "type": "fasta"
|
|
134 },
|
|
135 {
|
|
136 "name": "repeat_sequences_only",
|
|
137 "type": "fasta"
|
|
138 },
|
|
139 {
|
|
140 "name": "discarded_sequences",
|
|
141 "type": "fasta"
|
|
142 },
|
|
143 {
|
|
144 "name": "summary",
|
|
145 "type": "txt"
|
|
146 }
|
|
147 ],
|
|
148 "position": {
|
|
149 "left": 1036,
|
|
150 "top": 200
|
|
151 },
|
|
152 "post_job_actions": {},
|
|
153 "tool_errors": null,
|
|
154 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/aaronpetkau/filter_spades_repeats/filter_spades_repeat/1.0.0",
|
|
155 "tool_state": "{\"__page__\": 0, \"len_cutoff\": \"\\\"1000\\\"\", \"rep_cutoff\": \"\\\"1.75\\\"\", \"__rerun_remap_job_id__\": null, \"keep_leftover\": \"\\\"yes\\\"\", \"tab_input\": \"null\", \"cov_len_cutoff\": \"\\\"5000\\\"\", \"print_summary\": \"\\\"yes\\\"\", \"cov_cutoff\": \"\\\"0.33\\\"\", \"fasta_input\": \"null\"}",
|
|
156 "tool_version": "1.0.0",
|
|
157 "type": "tool",
|
|
158 "user_outputs": [],
|
|
159 "uuid": "19c772f8-7e42-4195-8cbb-bdccd2a5cedb"
|
|
160 },
|
|
161 "4": {
|
|
162 "annotation": "",
|
|
163 "id": 4,
|
|
164 "input_connections": {
|
|
165 "input": {
|
|
166 "id": 3,
|
|
167 "output_name": "output_with_repeats"
|
|
168 }
|
|
169 },
|
|
170 "inputs": [],
|
|
171 "label": null,
|
|
172 "name": "assemblystats",
|
|
173 "outputs": [
|
|
174 {
|
|
175 "name": "stats",
|
|
176 "type": "tabular"
|
|
177 },
|
|
178 {
|
|
179 "name": "sortedcontigs",
|
|
180 "type": "fasta"
|
|
181 },
|
|
182 {
|
|
183 "name": "histogrampng",
|
|
184 "type": "png"
|
|
185 },
|
|
186 {
|
|
187 "name": "summedcontigspng",
|
|
188 "type": "png"
|
|
189 },
|
|
190 {
|
|
191 "name": "histogramdata",
|
|
192 "type": "tabular"
|
|
193 },
|
|
194 {
|
|
195 "name": "summedcontigdata",
|
|
196 "type": "tabular"
|
|
197 }
|
|
198 ],
|
|
199 "position": {
|
|
200 "left": 1320,
|
|
201 "top": 200
|
|
202 },
|
|
203 "post_job_actions": {},
|
|
204 "tool_errors": null,
|
|
205 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/aaronpetkau/assemblystats/assemblystats/1.0.2",
|
|
206 "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"contig\\\"\", \"__rerun_remap_job_id__\": null, \"bucket\": \"\\\"False\\\"\", \"all_outputs\": \"\\\"False\\\"\", \"input\": \"null\"}",
|
|
207 "tool_version": "1.0.2",
|
|
208 "type": "tool",
|
|
209 "user_outputs": [],
|
|
210 "uuid": "07c871e9-4509-4c84-a479-8b597774af0e"
|
|
211 }
|
|
212 },
|
|
213 "uuid": "5a9d63ba-cab7-4dc7-8cbc-2131d87a837d"
|
|
214 } |