|
7
|
1 {
|
|
|
2 "a_galaxy_workflow": "true",
|
|
|
3 "annotation": "",
|
|
|
4 "format-version": "0.1",
|
|
|
5 "name": "Phenix workflow",
|
|
|
6 "steps": {
|
|
|
7 "0": {
|
|
|
8 "annotation": "",
|
|
|
9 "content_id": null,
|
|
|
10 "id": 0,
|
|
|
11 "input_connections": {},
|
|
|
12 "inputs": [
|
|
|
13 {
|
|
|
14 "description": "",
|
|
|
15 "name": "ref fa"
|
|
|
16 }
|
|
|
17 ],
|
|
|
18 "label": null,
|
|
|
19 "name": "Input dataset",
|
|
|
20 "outputs": [],
|
|
|
21 "position": {
|
|
|
22 "left": 200,
|
|
|
23 "top": 136.5
|
|
|
24 },
|
|
|
25 "tool_errors": null,
|
|
|
26 "tool_id": null,
|
|
|
27 "tool_state": "{\"name\": \"ref fa\"}",
|
|
|
28 "tool_version": null,
|
|
|
29 "type": "data_input",
|
|
|
30 "uuid": "b7ff9ad4-b07e-4c50-a38e-de10113b7314",
|
|
|
31 "workflow_outputs": []
|
|
|
32 },
|
|
|
33 "1": {
|
|
|
34 "annotation": "",
|
|
|
35 "content_id": null,
|
|
|
36 "id": 1,
|
|
|
37 "input_connections": {},
|
|
|
38 "inputs": [
|
|
|
39 {
|
|
|
40 "description": "",
|
|
|
41 "name": "r1"
|
|
|
42 }
|
|
|
43 ],
|
|
|
44 "label": null,
|
|
|
45 "name": "Input dataset",
|
|
|
46 "outputs": [],
|
|
|
47 "position": {
|
|
|
48 "left": 205,
|
|
|
49 "top": 273.5
|
|
|
50 },
|
|
|
51 "tool_errors": null,
|
|
|
52 "tool_id": null,
|
|
|
53 "tool_state": "{\"name\": \"r1\"}",
|
|
|
54 "tool_version": null,
|
|
|
55 "type": "data_input",
|
|
|
56 "uuid": "730623b2-2780-4de8-aa64-20949d734754",
|
|
|
57 "workflow_outputs": []
|
|
|
58 },
|
|
|
59 "2": {
|
|
|
60 "annotation": "",
|
|
|
61 "content_id": null,
|
|
|
62 "id": 2,
|
|
|
63 "input_connections": {},
|
|
|
64 "inputs": [
|
|
|
65 {
|
|
|
66 "description": "",
|
|
|
67 "name": "r2"
|
|
|
68 }
|
|
|
69 ],
|
|
|
70 "label": null,
|
|
|
71 "name": "Input dataset",
|
|
|
72 "outputs": [],
|
|
|
73 "position": {
|
|
|
74 "left": 209,
|
|
|
75 "top": 406.5
|
|
|
76 },
|
|
|
77 "tool_errors": null,
|
|
|
78 "tool_id": null,
|
|
|
79 "tool_state": "{\"name\": \"r2\"}",
|
|
|
80 "tool_version": null,
|
|
|
81 "type": "data_input",
|
|
|
82 "uuid": "f7d572ac-c3fc-4bb1-97fc-641460c32139",
|
|
|
83 "workflow_outputs": []
|
|
|
84 },
|
|
|
85 "3": {
|
|
|
86 "annotation": "",
|
|
|
87 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2",
|
|
|
88 "id": 3,
|
|
|
89 "input_connections": {
|
|
|
90 "fastq_input|fastq_input1": {
|
|
|
91 "id": 1,
|
|
|
92 "output_name": "output"
|
|
|
93 },
|
|
|
94 "fastq_input|fastq_input2": {
|
|
|
95 "id": 2,
|
|
|
96 "output_name": "output"
|
|
|
97 },
|
|
|
98 "reference_source|ref_file": {
|
|
|
99 "id": 0,
|
|
|
100 "output_name": "output"
|
|
|
101 }
|
|
|
102 },
|
|
|
103 "inputs": [],
|
|
|
104 "label": null,
|
|
|
105 "name": "Map with BWA-MEM",
|
|
|
106 "outputs": [
|
|
|
107 {
|
|
|
108 "name": "bam_output",
|
|
|
109 "type": "bam"
|
|
|
110 }
|
|
|
111 ],
|
|
|
112 "position": {
|
|
|
113 "left": 443,
|
|
|
114 "top": 203.5
|
|
|
115 },
|
|
|
116 "post_job_actions": {},
|
|
|
117 "tool_errors": null,
|
|
|
118 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2",
|
|
|
119 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\"}",
|
|
|
120 "tool_version": "0.4.2",
|
|
|
121 "type": "tool",
|
|
|
122 "uuid": "1896896c-a5c5-408b-8f43-54fb3d466e59",
|
|
|
123 "workflow_outputs": []
|
|
|
124 },
|
|
|
125 "4": {
|
|
|
126 "annotation": "",
|
|
|
127 "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
|
|
|
128 "id": 4,
|
|
|
129 "input_connections": {
|
|
|
130 "input_bam": {
|
|
|
131 "id": 3,
|
|
|
132 "output_name": "bam_output"
|
|
|
133 },
|
|
|
134 "ref_file": {
|
|
|
135 "id": 0,
|
|
|
136 "output_name": "output"
|
|
|
137 }
|
|
|
138 },
|
|
|
139 "inputs": [],
|
|
|
140 "label": null,
|
|
|
141 "name": "PHE MPileup",
|
|
|
142 "outputs": [
|
|
|
143 {
|
|
|
144 "name": "outvcf",
|
|
|
145 "type": "vcf"
|
|
|
146 }
|
|
|
147 ],
|
|
|
148 "position": {
|
|
|
149 "left": 456,
|
|
|
150 "top": 425.5
|
|
|
151 },
|
|
|
152 "post_job_actions": {},
|
|
|
153 "tool_errors": null,
|
|
|
154 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0",
|
|
|
155 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}",
|
|
|
156 "tool_version": "1.0",
|
|
|
157 "type": "tool",
|
|
|
158 "uuid": "dd975120-5a22-467b-a8f7-cc801faccfd6",
|
|
|
159 "workflow_outputs": []
|
|
|
160 },
|
|
|
161 "5": {
|
|
|
162 "annotation": "",
|
|
|
163 "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
|
|
|
164 "id": 5,
|
|
|
165 "input_connections": {
|
|
|
166 "input": {
|
|
|
167 "id": 4,
|
|
|
168 "output_name": "outvcf"
|
|
|
169 }
|
|
|
170 },
|
|
|
171 "inputs": [],
|
|
|
172 "label": null,
|
|
|
173 "name": "Filter VCF",
|
|
|
174 "outputs": [
|
|
|
175 {
|
|
|
176 "name": "output",
|
|
|
177 "type": "vcf"
|
|
|
178 }
|
|
|
179 ],
|
|
|
180 "position": {
|
|
|
181 "left": 666,
|
|
|
182 "top": 379.5
|
|
|
183 },
|
|
|
184 "post_job_actions": {},
|
|
|
185 "tool_errors": null,
|
|
|
186 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0",
|
|
|
187 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"gq_score\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"snp_filter_type_selector\\\": \\\"gq_score_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\", \"__page__\": 0}",
|
|
|
188 "tool_version": "1.0",
|
|
|
189 "type": "tool",
|
|
|
190 "uuid": "36480e46-74dd-4bb7-b350-c3e75f4f2354",
|
|
|
191 "workflow_outputs": []
|
|
|
192 }
|
|
|
193 },
|
|
|
194 "uuid": "15c9a48b-931d-4ff6-b12f-4c9a1affea2e"
|
|
|
195 } |
