comparison assembly_single_end_workflow.ga @ 0:473e5ce08c42 draft

Uploaded
author aaronpetkau
date Sun, 05 Jul 2015 06:08:56 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:473e5ce08c42
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 }