Mercurial > repos > dereeper > haplotype_analysis_workflow

comparison Galaxy-Workflow-Haplotype_analysis.ga @ 0:f81b8b6a97fb draft

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planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f-dirty
author dereeper
date Tue, 14 Aug 2018 08:32:12 -0400
parents
children bd20187f16c5
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-1:000000000000 0:f81b8b6a97fb
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Haplotype_analysis",
6 "steps": {
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11 "id": 0,
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13 "inputs": [
14 {
15 "description": "runtime parameter for tool VCFtools Filter",
16 "name": "input"
17 }
18 ],
19 "label": null,
20 "name": "VCFtools Filter",
21 "outputs": [
22 {
23 "name": "fileout",
24 "type": "vcf"
25 },
26 {
27 "name": "fileout_map",
28 "type": "tabular"
29 },
30 {
31 "name": "filelog",
32 "type": "txt"
33 }
34 ],
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39 "post_job_actions": {},
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41 "tool_shed_repository": {
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43 "name": "vcftools_filter_stats_diversity",
44 "owner": "vmarcon",
45 "tool_shed": "testtoolshed.g2.bx.psu.edu"
46 },
47 "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"3\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"4\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}",
48 "tool_version": "2.0.0",
49 "type": "tool",
50 "uuid": "4a63fe7d-03bf-4f8a-b744-acc6c333fd56",
51 "workflow_outputs": []
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53 "1": {
54 "annotation": "",
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56 "errors": null,
57 "id": 1,
58 "input_connections": {
59 "vcf_input": {
60 "id": 0,
61 "output_name": "fileout"
62 }
63 },
64 "inputs": [
65 {
66 "description": "runtime parameter for tool Beagle",
67 "name": "vcf_input"
68 }
69 ],
70 "label": null,
71 "name": "Beagle",
72 "outputs": [
73 {
74 "name": "vcf_ouput",
75 "type": "vcf"
76 },
77 {
78 "name": "log",
79 "type": "txt"
80 }
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88 "tool_shed_repository": {
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90 "name": "beagle",
91 "owner": "vmarcon",
92 "tool_shed": "testtoolshed.g2.bx.psu.edu"
93 },
94 "tool_state": "{\"phase\": \"\\\"5\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"impute\": \"\\\"5\\\"\", \"vcf_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
95 "tool_version": "1.0.0",
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98 "workflow_outputs": []
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100 "2": {
101 "annotation": "",
102 "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/sniplay/getHaplotypesFromPhasedVCF/2.0.0",
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104 "id": 2,
105 "input_connections": {
106 "input": {
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108 "output_name": "vcf_ouput"
109 }
110 },
111 "inputs": [
112 {
113 "description": "runtime parameter for tool Get Haplotypes From Phased VCF",
114 "name": "input"
115 }
116 ],
117 "label": null,
118 "name": "Get Haplotypes From Phased VCF",
119 "outputs": [
120 {
121 "name": "output_distinct",
122 "type": "txt"
123 },
124 {
125 "name": "output_haplo",
126 "type": "fasta"
127 },
128 {
129 "name": "output_distinct_fasta",
130 "type": "fasta"
131 }
132 ],
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137 "post_job_actions": {},
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141 "name": "sniplay",
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146 "tool_version": "2.0.0",
147 "type": "tool",
148 "uuid": "4bfbaba7-3fc2-4076-82d6-3212c61fcb91",
149 "workflow_outputs": []
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154 "errors": null,
155 "id": 3,
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157 "input": {
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159 "output_name": "output_distinct_fasta"
160 }
161 },
162 "inputs": [
163 {
164 "description": "runtime parameter for tool Haplophyle",
165 "name": "input"
166 }
167 ],
168 "label": null,
169 "name": "Haplophyle",
170 "outputs": [
171 {
172 "name": "fileout",
173 "type": "json"
174 },
175 {
176 "name": "dotfile",
177 "type": "txt"
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179 {
180 "name": "filelog",
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192 "name": "haplophyle",
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197 "tool_version": "1.0.0",
198 "type": "tool",
199 "uuid": "31d5583a-740b-46e2-80d8-02d0315ac954",
200 "workflow_outputs": []
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223 "name": "cytoscape_html",
224 "type": "html"
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226 {
227 "name": "filelog",
228 "type": "txt"
229 }
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247 "workflow_outputs": []
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250 "tags": [],
251 "uuid": "2ce7df85-4151-40cc-b636-a135663b90ee"
252 }