Mercurial > repos > wolma > mimodd_workflows

comparison Galaxy-Workflow-MiModD_example_workflow_1.ga @ 0:9f64313f2ccb

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author wolma
date Wed, 11 Feb 2015 10:06:13 -0500
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children 87bfe31ce878
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-1:000000000000 0:9f64313f2ccb
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "MiModD example workflow 1",
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 ],
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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 },
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61 "id": 2,
62 "input_connections": {
63 "list_input_0|inputfile": {
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66 },
67 "ref_genome": {
68 "id": 0,
69 "output_name": "output"
70 }
71 },
72 "inputs": [],
73 "name": "Variant Calling",
74 "outputs": [
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76 "name": "output_vcf",
77 "type": "bcf"
78 }
79 ],
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82 "top": 364
83 },
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89 "type": "tool",
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91 },
92 "3": {
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96 "ifile": {
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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 },
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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}",
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118 "type": "tool",
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120 },
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128 }
129 },
130 "inputs": [],
131 "name": "Coverage Statistics",
132 "outputs": [
133 {
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135 "type": "tabular"
136 }
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140 "top": 455
141 },
142 "post_job_actions": {},
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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": {
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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 }