Mercurial > repos > wolma > mimodd_workflows
comparison Galaxy-Workflow-MiModD_example_workflow_3.ga @ 0:9f64313f2ccb
Uploaded
author | wolma |
---|---|
date | Wed, 11 Feb 2015 10:06:13 -0500 |
parents | |
children | 87bfe31ce878 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9f64313f2ccb |
---|---|
1 { | |
2 "a_galaxy_workflow": "true", | |
3 "annotation": "", | |
4 "format-version": "0.1", | |
5 "name": "MiModD example workflow 3", | |
6 "steps": { | |
7 "0": { | |
8 "annotation": "", | |
9 "id": 0, | |
10 "input_connections": {}, | |
11 "inputs": [ | |
12 { | |
13 "description": "", | |
14 "name": "Input Dataset" | |
15 } | |
16 ], | |
17 "name": "Input dataset", | |
18 "outputs": [], | |
19 "position": { | |
20 "left": 172, | |
21 "top": 176 | |
22 }, | |
23 "tool_errors": null, | |
24 "tool_id": null, | |
25 "tool_state": "{\"name\": \"Input Dataset\"}", | |
26 "tool_version": null, | |
27 "type": "data_input", | |
28 "user_outputs": [] | |
29 }, | |
30 "1": { | |
31 "annotation": "", | |
32 "id": 1, | |
33 "input_connections": { | |
34 "ref_genome": { | |
35 "id": 0, | |
36 "output_name": "output" | |
37 } | |
38 }, | |
39 "inputs": [], | |
40 "name": "SNAP Read Alignment", | |
41 "outputs": [ | |
42 { | |
43 "name": "outputfile", | |
44 "type": "bam" | |
45 } | |
46 ], | |
47 "position": { | |
48 "left": 359, | |
49 "top": 368 | |
50 }, | |
51 "post_job_actions": {}, | |
52 "tool_errors": null, | |
53 "tool_id": "read_alignment", | |
54 "tool_state": "{\"__page__\": 0, \"datasets\": \"[{\\\"__index__\\\": 0, \\\"mode_choose\\\": {\\\"input\\\": {\\\"header\\\": null, \\\"ifile\\\": null, \\\"iformat\\\": \\\"bam\\\", \\\"__current_case__\\\": 0}, \\\"mode\\\": \\\"paired\\\", \\\"__current_case__\\\": 1}}]\", \"__rerun_remap_job_id__\": null, \"set\": \"{\\\"sort\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"clipping\\\": \\\"++\\\", \\\"filter_output\\\": \\\"off\\\", \\\"confadpt\\\": \\\"7\\\", \\\"slack\\\": \\\"0.3\\\", \\\"maxdist\\\": \\\"8\\\", \\\"maxseeds\\\": \\\"25\\\", \\\"maxhits\\\": \\\"250\\\", \\\"max_mate_overlap\\\": \\\"0\\\", \\\"selectivity\\\": \\\"off\\\", \\\"settings_mode\\\": \\\"default\\\", \\\"sp_min\\\": \\\"100\\\", \\\"sp_max\\\": \\\"10000\\\", \\\"seedsize\\\": \\\"20\\\", \\\"mmatch_notation\\\": \\\"general\\\", \\\"confdiff\\\": \\\"2\\\"}\", \"oformat\": \"\\\"bam\\\"\", \"ref_genome\": \"null\"}", | |
55 "tool_version": "1.0.0", | |
56 "type": "tool", | |
57 "user_outputs": [] | |
58 }, | |
59 "2": { | |
60 "annotation": "", | |
61 "id": 2, | |
62 "input_connections": { | |
63 "list_input_0|inputfile": { | |
64 "id": 1, | |
65 "output_name": "outputfile" | |
66 }, | |
67 "ref_genome": { | |
68 "id": 0, | |
69 "output_name": "output" | |
70 } | |
71 }, | |
72 "inputs": [], | |
73 "name": "Variant Calling", | |
74 "outputs": [ | |
75 { | |
76 "name": "output_vcf", | |
77 "type": "bcf" | |
78 } | |
79 ], | |
80 "position": { | |
81 "left": 708, | |
82 "top": 364 | |
83 }, | |
84 "post_job_actions": {}, | |
85 "tool_errors": null, | |
86 "tool_id": "variant_calling", | |
87 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"depth\": \"\\\"250\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"inputfile\\\": null}]\", \"ref_genome\": \"null\", \"no_md5_check\": \"\\\"False\\\"\"}", | |
88 "tool_version": "1.0.0", | |
89 "type": "tool", | |
90 "user_outputs": [] | |
91 }, | |
92 "3": { | |
93 "annotation": "", | |
94 "id": 3, | |
95 "input_connections": { | |
96 "ifile": { | |
97 "id": 2, | |
98 "output_name": "output_vcf" | |
99 } | |
100 }, | |
101 "inputs": [], | |
102 "name": "Extract Variant Sites", | |
103 "outputs": [ | |
104 { | |
105 "name": "output_vcf", | |
106 "type": "vcf" | |
107 } | |
108 ], | |
109 "position": { | |
110 "left": 1104.5, | |
111 "top": 227 | |
112 }, | |
113 "post_job_actions": {}, | |
114 "tool_errors": null, | |
115 "tool_id": "extract_variants", | |
116 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"keep_alts\": \"\\\"False\\\"\", \"sitesinfo\": \"[]\", \"__rerun_remap_job_id__\": null}", | |
117 "tool_version": "1.0.0", | |
118 "type": "tool", | |
119 "user_outputs": [] | |
120 }, | |
121 "4": { | |
122 "annotation": "", | |
123 "id": 4, | |
124 "input_connections": { | |
125 "ifile": { | |
126 "id": 2, | |
127 "output_name": "output_vcf" | |
128 } | |
129 }, | |
130 "inputs": [], | |
131 "name": "Coverage Statistics", | |
132 "outputs": [ | |
133 { | |
134 "name": "output_vcf", | |
135 "type": "tabular" | |
136 } | |
137 ], | |
138 "position": { | |
139 "left": 1133, | |
140 "top": 455 | |
141 }, | |
142 "post_job_actions": {}, | |
143 "tool_errors": null, | |
144 "tool_id": "coverage_stats", | |
145 "tool_state": "{\"__page__\": 0, \"ifile\": \"null\", \"__rerun_remap_job_id__\": null}", | |
146 "tool_version": "1.0.0", | |
147 "type": "tool", | |
148 "user_outputs": [] | |
149 }, | |
150 "5": { | |
151 "annotation": "", | |
152 "id": 5, | |
153 "input_connections": { | |
154 "covfile": { | |
155 "id": 2, | |
156 "output_name": "output_vcf" | |
157 }, | |
158 "list_input_0|bamfile": { | |
159 "id": 1, | |
160 "output_name": "outputfile" | |
161 } | |
162 }, | |
163 "inputs": [], | |
164 "name": "Deletion Prediction for paired-end data", | |
165 "outputs": [ | |
166 { | |
167 "name": "outputfile", | |
168 "type": "gff" | |
169 } | |
170 ], | |
171 "position": { | |
172 "left": 1064, | |
173 "top": 667 | |
174 }, | |
175 "post_job_actions": {}, | |
176 "tool_errors": null, | |
177 "tool_id": "deletion_prediction", | |
178 "tool_state": "{\"__page__\": 0, \"group_by_id\": \"\\\"True\\\"\", \"__rerun_remap_job_id__\": null, \"min_size\": \"\\\"100\\\"\", \"list_input\": \"[{\\\"__index__\\\": 0, \\\"bamfile\\\": null}]\", \"include_uncovered\": \"\\\"False\\\"\", \"covfile\": \"null\", \"max_cov\": \"\\\"4\\\"\"}", | |
179 "tool_version": "1.0.0", | |
180 "type": "tool", | |
181 "user_outputs": [] | |
182 } | |
183 } | |
184 } |